X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details MMP12 AT 0.4 mM co-crystallization, with 100mM AHA and non-chelating inhibitor EEG at 1.1 mM with reservoir: 27% PEG 10K, 0.1M glycine. AHA removed during cryo-soak for 5 min in 30% MPEG2K, 10% ethylene glycol, 200 mM imidazole malate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.09 α = 90
b = 63.65 β = 90
c = 37.37 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 bent cylindrical mirror 2009-07-20
Diffraction Radiation
Monochromator Protocol
horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.99190 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
1.59 33 99.6 0.099 0.081 -- 7.67 23301 23208 0.0 0.0 25.7
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)
1.59 1.68 98.8 0.632 0.805 2.89 7.58 3687

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 1.587 32.976 -- 2.01 23295 23181 1160 99.51 -- 0.1797 0.1784 0.203 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 1.5871 1.6594 -- 140 2654 0.2762 0.2966 -- 98.0
X Ray Diffraction 1.6594 1.7468 -- 144 2730 0.2271 0.2571 -- 100.0
X Ray Diffraction 1.7468 1.8563 -- 143 2736 0.1984 0.206 -- 100.0
X Ray Diffraction 1.8563 1.9996 -- 143 2724 0.1776 0.1857 -- 100.0
X Ray Diffraction 1.9996 2.2008 -- 146 2755 0.177 0.214 -- 100.0
X Ray Diffraction 2.2008 2.5191 -- 144 2742 0.1813 0.2104 -- 100.0
X Ray Diffraction 2.5191 3.1734 -- 148 2806 0.1757 0.2222 -- 100.0
X Ray Diffraction 3.1734 32.9828 -- 152 2874 0.159 0.1739 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic (TLS)
Anisotropic B[1][1] 0.3654
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1928
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1726
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 1.612
f_dihedral_angle_d 18.681
f_chiral_restr 0.095
f_bond_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 213

Software

Software
Software Name Purpose
DNA data collection
MOLREP phasing
PHENIX refinement version: (phenix.refine)
XDS data reduction
XSCALE data scaling