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
CCD 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_scangle_it 5.809
r_scbond_it 3.74
r_mcangle_it 2.682
r_mcbond_it 1.613
r_gen_planes_refined 0.016
r_chiral_restr 0.182
r_dihedral_angle_4_deg 21.192
r_dihedral_angle_3_deg 14.826
r_dihedral_angle_2_deg 35.385
r_dihedral_angle_1_deg 6.638
r_angle_refined_deg 2.607
r_bond_refined_d 0.029
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

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