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_gen_planes_other 0.003
r_mcbond_it 1.372
r_scbond_it 3.131
r_scangle_it 4.865
r_angle_other_deg 1.033
r_dihedral_angle_2_deg 35.842
r_angle_refined_deg 2.038
r_mcangle_it 2.29
r_dihedral_angle_1_deg 7.055
r_dihedral_angle_4_deg 18.651
r_bond_refined_d 0.022
r_chiral_restr 0.114
r_gen_planes_refined 0.011
r_mcbond_other 0.414
r_bond_other_d 0.002
r_dihedral_angle_3_deg 16.634
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

Software
Software Name Purpose
DNA data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
XDS data reduction
XDS data scaling