X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details protein: hMMP-9-WT at 2 mg/mL with 120 milli-M acetohydroxamic acid. Reservoir: 40% monomethyl PEG 5,000, 0.1 M glycine. Cryoprotectant: 35% MPEG 5K, 15% PEG 400, 15% AAB buffer at pH 8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.18 α = 90
b = 97.4 β = 111.99
c = 45.69 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2010-12-20
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1

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
2.9 50 98.0 0.195 0.17 -- 4.15 7301 7158 0.0 -3.0 26.65
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)
2.9 3.08 96.5 0.53 0.463 2.9 4.12 1189

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
MOLREP 2.902 38.85 -3.0 2.0 7158 7128 357 98.03 -- 0.279 0.2771 0.3114 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 2.9025 3.3223 2238 118 2238 0.2665 0.3009 -- 97.0
X Ray Diffraction 3.3223 4.1849 2260 119 2260 0.2621 0.3218 -- 99.0
X Ray Diffraction 4.1849 38.8534 2273 120 2273 0.2979 0.3083 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model grouped/Isotropic
Mean Isotropic B 19.01
Anisotropic B[1][1] 0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.07
Anisotropic B[2][2] -1.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.17
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.084
f_dihedral_angle_d 26.662
f_angle_d 1.458
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2608
Nucleic Acid Atoms 0
Heterogen Atoms 199
Solvent Atoms 148

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)/REFMAC Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069)/REFMAC refinement
MOLREP model building
DNA data collection