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 - 0.53 mM F67D mutant of human MMP12 residues 106-263 in 0.1 M acetohydroxamic acid 0.003 M CaCl2, 0.200 M NaCl 0.02 M Tris-HCl, pH 7.5. Reservoir solution -27% PEG 10K,0.2 M imidazole malate cryoconditions - CryoProtX-Cryomix 7, 25% MPEG 5K, 0.1 M AAB 10/90, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.97 α = 90
b = 63.19 β = 90
c = 37.51 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
PIXEL PSI PILATUS 6M mirrors 2012-02-17
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 0.918400 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
1.63 46.59 97.4 0.086 0.083 -- 8.72 21260 20710 0.0 0.0 25.023
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)
1.63 1.72 99.3 0.726 0.683 3.31 8.55 3230

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
RIGID BODY 1.63 46.59 -3.0 0.0 21260 20063 1056 100.0 -- 0.15554 0.15368 0.19044 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 1.626 1.669 -- 71 1352 0.263 0.365 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 20.811
Anisotropic B[1][1] -1.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.35
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.613
r_dihedral_angle_3_deg 14.826
r_dihedral_angle_1_deg 6.638
r_gen_planes_refined 0.016
r_bond_refined_d 0.029
r_angle_refined_deg 2.607
r_dihedral_angle_4_deg 21.192
r_scbond_it 3.74
r_dihedral_angle_2_deg 35.385
r_chiral_restr 0.182
r_scangle_it 5.809
r_mcangle_it 2.682
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 139

Software

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