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 848 microM. reservoir: 24% PEG 10000, 0.2 M imidazole malate pH 8.5. CRYOPROTECTANT: 27% PEG 8000, 15% monomethyl-PEG 550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.83 α = 90
b = 61.47 β = 90
c = 33.46 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 315r mirrors 2010-04-24
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9765 ESRF ID14-4

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
1.3 50 99.4 0.098 0.091 -- 7.56 35305 35086 0.0 -4.0 17.669
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)
1.3 1.38 97.7 0.86 0.798 2.47 7.16 5602

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 1.299 30.008 -3.0 1.99 35086 35069 1753 99.37 -- 0.178 0.1767 0.2027 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 1.2988 1.3339 2411 125 2411 0.2661 0.279 -- 96.0
X Ray Diffraction 1.3339 1.3732 2546 134 2546 0.2353 0.2661 -- 100.0
X Ray Diffraction 1.3732 1.4175 2526 133 2526 0.2194 0.2398 -- 100.0
X Ray Diffraction 1.4175 1.4681 2540 134 2540 0.208 0.2395 -- 100.0
X Ray Diffraction 1.4681 1.5269 2553 135 2553 0.2057 0.2421 -- 100.0
X Ray Diffraction 1.5269 1.5964 2556 134 2556 0.185 0.2034 -- 100.0
X Ray Diffraction 1.5964 1.6806 2554 135 2554 0.1778 0.2067 -- 100.0
X Ray Diffraction 1.6806 1.7859 2547 134 2547 0.1794 0.183 -- 100.0
X Ray Diffraction 1.7859 1.9237 2569 135 2569 0.1658 0.1999 -- 100.0
X Ray Diffraction 1.9237 2.1173 2598 137 2598 0.165 0.197 -- 100.0
X Ray Diffraction 2.1173 2.4235 2593 136 2593 0.1697 0.1913 -- 100.0
X Ray Diffraction 2.4235 3.0529 2635 139 2635 0.172 0.2091 -- 100.0
X Ray Diffraction 3.0529 30.0156 2688 142 2688 0.1577 0.1789 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.077
f_dihedral_angle_d 16.521
f_angle_d 1.154
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1191
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 197

Software

Computing
Computing Package Purpose
CBASS 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
CBASS data collection