Startup.cs

using Microsoft.Owin;
using Owin;
using System.Web.Http;
using IdentityServer3.AccessTokenValidation;
using IdentityServer3.Core.Configuration;
using IdSrv;

[assembly: OwinStartup(typeof(Apis.Startup))]

namespace Apis
{
    public class Startup
    {
        public void Configuration(IAppBuilder app)
        {
            app.Map("/identity", idsrvApp =>
            {
                var options = new IdentityServerOptions
                {
                    Factory = new IdentityServerServiceFactory()
                        .UseInMemoryClients(Clients.Get())
                        .UseInMemoryScopes(Scopes.Get())
                        .UseInMemoryUsers(Users.Get()),
                    RequireSsl = false
                };
                app.UseIdentityServer(options);
            });

            // accept access tokens from identityserver and require a scope of 'api1'
            app.UseIdentityServerBearerTokenAuthentication(new IdentityServerBearerTokenAuthenticationOptions
            {
                Authority = "http://localhost:14869/identity",
                ValidationMode = ValidationMode.Local,
                RequiredScopes = new[] { "api1" }
            });

            // configure web api
            var config = new HttpConfiguration();
            config.MapHttpAttributeRoutes();
            
            // require authentication for all controllers
            config.Filters.Add(new AuthorizeAttribute());

            app.UseWebApi(config);
        }
    }
}

NB: Assume this is hosted at localhost:14869