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 solution: 222 microM MMP12 mutant E219A 106 microM bifunctional inhibitor LD884. Reservoir: 27% PEG 10K, 150mM imidazole piperidine, pH 8.5. Cryoprotectant: 5 % di-ethylene glycol + 5 % ethylene glycol + 10 % 1,2-propanediol + 5 % DMSO + 5 % glycerol, 25% MPEG 5K, 100mM (Na acetate, ADA, Bicine 10% pH 4.0/90% pH 9.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.79 α = 90
b = 60.1 β = 116.67
c = 54.92 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M mirrors 2012-10-12
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 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
1.7 50 99.2 0.102 0.089 -- 4.14 16789 16663 0.0 -4.0 28.35
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)
1.7 1.8 97.2 0.887 0.768 1.71 4.02 2693

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 1.7 36.67 -4.0 0.0 16663 15828 834 100.0 -- 0.14626 0.14361 0.19397 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 1.696 1.74 -- 60 1124 0.252 0.296 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 19.56
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.06
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.865
r_scbond_it 3.131
r_mcangle_it 2.29
r_mcbond_other 0.414
r_bond_refined_d 0.022
r_bond_other_d 0.002
r_angle_refined_deg 2.038
r_angle_other_deg 1.033
r_dihedral_angle_1_deg 7.055
r_dihedral_angle_2_deg 35.842
r_dihedral_angle_3_deg 16.634
r_dihedral_angle_4_deg 18.651
r_chiral_restr 0.114
r_gen_planes_refined 0.011
r_gen_planes_other 0.003
r_mcbond_it 1.372
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1242
Nucleic Acid Atoms 0
Heterogen Atoms 139
Solvent Atoms 171

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
MOLREP model building
DNA data collection