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 complex: hMMP12 F171D 855 microM, inhibitor 0.788 milliM. Reservoir: 35% PEG 4,000 0.2M imidazole malate pH 8.5. Drops: 1 microL protein complex + 1 microL reservoir. Cryoprotectant: 40% MPEG 5K, 10% 1,2-propanediol, (10% (Na acetate, ADA, Bicine) 90% at pH 4/ 10% at pH 9.0). Flash freezing in Liquid N2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.77 α = 90
b = 62.76 β = 90
c = 37.84 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 ADSC QUANTUM 4r mirrors 2010-04-24
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
1.5 50 95.6 0.111 0.0976 -- 3.51 27502 26347 0.0 0.0 20.815
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)
1.5 1.59 77.7 1.04 0.849 1.19 2.88 4388

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 1.497 32.406 -3.0 1.99 26347 26336 1317 95.79 -- 0.188 0.1864 0.2178 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 1.497 1.5569 2095 110 2095 0.3188 0.3971 -- 73.0
X Ray Diffraction 1.5569 1.6277 2648 139 2648 0.2808 0.3282 -- 93.0
X Ray Diffraction 1.6277 1.7136 2830 149 2830 0.2481 0.2847 -- 99.0
X Ray Diffraction 1.7136 1.8209 2825 149 2825 0.2182 0.263 -- 99.0
X Ray Diffraction 1.8209 1.9615 2860 151 2860 0.1927 0.2093 -- 99.0
X Ray Diffraction 1.9615 2.1588 2877 151 2877 0.168 0.2084 -- 100.0
X Ray Diffraction 2.1588 2.4711 2896 152 2896 0.1723 0.2082 -- 100.0
X Ray Diffraction 2.4711 3.113 2915 154 2915 0.1684 0.1977 -- 100.0
X Ray Diffraction 3.113 32.4131 3073 162 3073 0.1566 0.177 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 11.4
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.077
f_dihedral_angle_d 15.251
f_angle_d 1.107
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 193

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
MOLREP model building
DNA data collection