X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details Protein: hMMP12(F171D) 643 microM. Reservoir: 18% PEG 10000, 0.2 M imidazole malate pH 8.0. Cryoprotectant: 27% PEG 8000, 15% monomethylPEG 550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.96 α = 90
b = 63.13 β = 90
c = 37.31 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Toroidal mirror 2009-09-20
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.9334 ESRF ID14-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.49 50 99.7 0.106 0.099 -- 7.9 27105 27049 0.0 -4.0 21.514
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.49 1.58 98.9 1.17 1.1 1.97 6.98 4273

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.494 46.565 -3.0 2.0 27049 27033 1352 99.76 -- 0.1821 0.1803 0.2158 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.4942 1.5476 2482 131 2482 0.2757 0.3122 -- 98.0
X Ray Diffraction 1.5476 1.6096 2511 132 2511 0.2477 0.2894 -- 100.0
X Ray Diffraction 1.6096 1.6828 2549 134 2549 0.2265 0.2741 -- 100.0
X Ray Diffraction 1.6828 1.7715 2540 133 2540 0.214 0.2571 -- 100.0
X Ray Diffraction 1.7715 1.8825 2546 135 2546 0.1931 0.2598 -- 100.0
X Ray Diffraction 1.8825 2.0279 2567 135 2567 0.1814 0.2178 -- 100.0
X Ray Diffraction 2.0279 2.232 2560 134 2560 0.174 0.2163 -- 100.0
X Ray Diffraction 2.232 2.5549 2567 136 2567 0.1702 0.2171 -- 100.0
X Ray Diffraction 2.5549 3.2188 2611 137 2611 0.1633 0.187 -- 100.0
X Ray Diffraction 3.2188 46.5872 2748 145 2748 0.159 0.1828 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.073
f_dihedral_angle_d 16.814
f_angle_d 1.091
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 295

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
MOLREP model building
DNA data collection