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: hMMP12 F171D 0.78 milli-M + 0.010 M AHA. Reservoir: 17% PEG 20.000, 0.2 M imidazole malate, pH 6.0, 0.25 M NaCl. Cryoprotectant: 10% di-ethylene glycol + 10% glycerol + 10% 1,2-propanediol, 25% M PEG 5.000, 0.1 M BES pH 5.5., VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.44 α = 90
b = 106.49 β = 94.96
c = 65.88 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M mirrors 2012-07-04
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
2.16 50 99.3 0.112 0.101 -- 5.63 35072 34818 0.0 -3.0 39.239
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)
2.16 2.29 96.0 0.696 0.698 2.6 5.46 5614

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 2.16 47.262 -3.0 2.0 34818 34809 1740 99.25 -- 0.1703 0.1667 0.2407 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 2.1573 2.2208 2507 132 2507 0.225 0.3442 -- 92.0
X Ray Diffraction 2.2208 2.2925 2787 146 2787 0.2225 0.305 -- 100.0
X Ray Diffraction 2.2925 2.3744 2757 146 2757 0.2082 0.2895 -- 100.0
X Ray Diffraction 2.3744 2.4695 2769 145 2769 0.196 0.3151 -- 100.0
X Ray Diffraction 2.4695 2.5819 2752 145 2752 0.1906 0.2724 -- 100.0
X Ray Diffraction 2.5819 2.718 2789 147 2789 0.1872 0.2512 -- 100.0
X Ray Diffraction 2.718 2.8883 2755 145 2755 0.1813 0.2964 -- 100.0
X Ray Diffraction 2.8883 3.1112 2775 146 2775 0.1872 0.2781 -- 100.0
X Ray Diffraction 3.1112 3.4242 2798 147 2798 0.1675 0.2528 -- 100.0
X Ray Diffraction 3.4242 3.9195 2769 146 2769 0.143 0.19 -- 100.0
X Ray Diffraction 3.9195 4.9374 2787 147 2787 0.1266 0.2023 -- 100.0
X Ray Diffraction 4.9374 47.2737 2824 148 2824 0.1566 0.1964 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 30.24
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.018
f_chiral_restr 0.07
f_dihedral_angle_d 16.194
f_angle_d 1.104
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4965
Nucleic Acid Atoms 0
Heterogen Atoms 196
Solvent Atoms 274

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