X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details MMP12 at 4mg/ml co-crystallization with non-chelating inhibitor with precipitant: 22% PEG 3350, 100mM Glycine., pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69 α = 90
b = 63.17 β = 90
c = 37.57 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 2008-06-14
Diffraction Radiation
Monochromator Protocol
Single Silicon (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1

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
1.9 69 99.5 0.128 0.059 -- 5.7 13486 13419 1.0 2.0 14.58
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)
1.9 2.0 100.0 0.534 0.589 4.2 5.8 1933

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
rigid body 1.9 46.592 -- 1.39 -- 13391 660 99.13 -- 0.161 0.1586 0.2105 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 1.9001 2.0468 -- 147 2496 0.1814 0.2393 -- 100.0
X Ray Diffraction 2.0468 2.2527 -- 121 2529 0.1537 0.1799 -- 100.0
X Ray Diffraction 2.2527 2.5787 -- 129 2526 0.1469 0.2156 -- 100.0
X Ray Diffraction 2.5787 3.2488 -- 145 2543 0.1504 0.1999 -- 99.0
X Ray Diffraction 3.2488 46.6065 -- 118 2637 0.1605 0.2069 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 17.788
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.081
f_dihedral_angle_d 18.163
f_angle_d 1.167
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 205

Software

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