3H8T
Structure of Porphyromonas gingivalis heme-binding protein HmuY in complex with Heme
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID23-1 |
Synchrotron site | ESRF |
Beamline | ID23-1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2008-07-18 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 1.0000 |
Spacegroup name | P 42 21 2 |
Unit cell lengths | 93.740, 93.740, 113.730 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.600 - 1.800 |
R-factor | 0.16057 |
Rwork | 0.160 |
R-free | 0.18709 |
Structure solution method | SIRAS |
RMSD bond length | 0.012 |
RMSD bond angle | 1.310 |
Data reduction software | XDS |
Data scaling software | SCALA |
Phasing software | SHELXDE |
Refinement software | REFMAC (5.5.0046) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.600 | 1.900 |
High resolution limit [Å] | 1.800 | 1.800 |
Rmerge | 0.101 | 0.669 |
Number of reflections | 47598 | |
<I/σ(I)> | 17.6 | 4.2 |
Completeness [%] | 100.0 | 99.9 |
Redundancy | 12.9 | 13.1 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Wilden / Innovadyne) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals as thin reddish prisms appeared in a Bruker steady-temperature crystal farm at 20 C using protein solution (26mg/mL in 5mM Tris/HCl, pH 8.0) and 2.4M (NH4)2SO4, 0.1M MES, pH6.0 as reservoir solution and D(+)-glucose monohydrate as additive (relative volumetric ratios 1:1:0.35). These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research). VAPOR DIFFUSION, SITTING DROP, temperature 293K |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Wilden / Innovadyne) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals as thin reddish prisms appeared in a Bruker steady-temperature crystal farm at 20 C using protein solution (26mg/mL in 5mM Tris/HCl, pH 8.0) and 2.4M (NH4)2SO4, 0.1M MES, pH6.0 as reservoir solution and D(+)-glucose monohydrate as additive (relative volumetric ratios 1:1:0.35). These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research). VAPOR DIFFUSION, SITTING DROP, temperature 293K |