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_chiral_restr 0.095
f_dihedral_angle_d 18.681
f_angle_d 1.612
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

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