X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details Protein: human MMP9 (E402Q) at 308.7 micro-M twin inhibitor LC20 at 154 micro-M (stoichiometry 2:1) and 120mM acetohydroxamic acid. RESERVOIR: 12% Polyethylene glycol 20,000, 1.5M NaCl, 0.1 M PCTP (Na propionate, Na cacodylate, Bis-Tris-propane ratio 2:1:2; 75% pH 4, 25% pH 9.5) CRYOPROTECTANT: 40% C2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 9% PEG 10,000 1.5M NaCl, 0.1M PCTP 80/2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.87 α = 90
b = 98.24 β = 90
c = 47.44 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 bent cylindrical mirror 2012-10-12
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
1.94 50 99.4 0.166 0.155 -- 7.98 26173 26019 0.0 -3.0 36.556
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)
1.94 2.06 96.6 1.533 1.432 1.3 7.87 4162

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 1.94 42.72 -3.0 0.0 26019 24713 1301 100.0 -- 0.21439 0.21088 0.28302 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 1.943 1.993 -- 88 1674 0.32 0.373 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 32.048
Anisotropic B[1][1] 0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 24.017
r_scangle_it 4.572
r_mcangle_it 2.12
r_dihedral_angle_2_deg 35.336
r_angle_refined_deg 1.966
r_chiral_restr 0.158
r_mcbond_it 1.241
r_dihedral_angle_1_deg 6.74
r_dihedral_angle_3_deg 16.531
r_bond_refined_d 0.022
r_scbond_it 3.114
r_gen_planes_refined 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2550
Nucleic Acid Atoms 0
Heterogen Atoms 190
Solvent Atoms 345

Software

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