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: hMMP12 F171D at 0.36 milli-M + 0.001 M AHA. Reservoir: 13% PEG 20,000 0.2 M imidazole malate 0.05 M NaCl Cryoprotectant: 27% PEG 8,000 15% MPEG 550, 10% glycerol, 0.09 M Tris-HCl , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.91 α = 90
b = 61.75 β = 90
c = 112.56 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M mirrors 2012-05-01
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.8856 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
1.43 50 99.7 0.059 0.053 -- 5.82 61962 61752 0.0 -3.0 21.616
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)
1.42 1.51 98.4 0.626 0.57 2.77 5.8 9880

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 1.43 43.31 -3.0 1.99 61752 61749 3087 99.66 -- 0.1577 0.1567 0.1767 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 1.4244 1.4467 2460 129 2460 0.227 0.223 -- 94.0
X Ray Diffraction 1.4467 1.4704 2675 141 2675 0.2062 0.2565 -- 100.0
X Ray Diffraction 1.4704 1.4958 2628 139 2628 0.1968 0.2057 -- 100.0
X Ray Diffraction 1.4958 1.523 2642 139 2642 0.1857 0.2159 -- 100.0
X Ray Diffraction 1.523 1.5523 2639 138 2639 0.1799 0.2021 -- 100.0
X Ray Diffraction 1.5523 1.584 2665 141 2665 0.1702 0.2023 -- 100.0
X Ray Diffraction 1.584 1.6184 2636 139 2636 0.1667 0.212 -- 100.0
X Ray Diffraction 1.6184 1.6561 2630 138 2630 0.1642 0.1744 -- 100.0
X Ray Diffraction 1.6561 1.6975 2615 138 2615 0.16 0.2138 -- 100.0
X Ray Diffraction 1.6975 1.7434 2673 140 2673 0.1571 0.189 -- 100.0
X Ray Diffraction 1.7434 1.7947 2663 140 2663 0.1555 0.1849 -- 100.0
X Ray Diffraction 1.7947 1.8526 2652 140 2652 0.1551 0.1896 -- 100.0
X Ray Diffraction 1.8526 1.9188 2662 140 2662 0.1463 0.1757 -- 100.0
X Ray Diffraction 1.9188 1.9956 2678 141 2678 0.1487 0.1632 -- 100.0
X Ray Diffraction 1.9956 2.0865 2650 140 2650 0.1411 0.1846 -- 100.0
X Ray Diffraction 2.0865 2.1965 2673 140 2673 0.1441 0.1709 -- 100.0
X Ray Diffraction 2.1965 2.3341 2692 142 2692 0.1523 0.1764 -- 100.0
X Ray Diffraction 2.3341 2.5143 2679 141 2679 0.1566 0.1812 -- 100.0
X Ray Diffraction 2.5143 2.7672 2719 143 2719 0.1568 0.1579 -- 100.0
X Ray Diffraction 2.7672 3.1676 2698 142 2698 0.1588 0.1807 -- 100.0
X Ray Diffraction 3.1676 3.9904 2760 145 2760 0.1405 0.1629 -- 100.0
X Ray Diffraction 3.9904 43.3202 2873 151 2873 0.1613 0.1585 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.078
f_dihedral_angle_d 16.272
f_angle_d 1.118
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2492
Nucleic Acid Atoms 0
Heterogen Atoms 127
Solvent Atoms 457

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