X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 10 MG/ML MBP-MCL1 VCID 9272, 200MM MG FORMATE, 20% PEG3350, 0.5M BRD-0611, 1MM MALTOSE, CRYOPROTECTANT 20% ETHYLENE GLYCOL

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.3 α = 90
b = 135.87 β = 90
c = 37.69 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 RIGAKU SATURN 944+ -- 2014-04-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54 -- --

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
1.85 50 99.7 0.062 -- -- 4.4 -- 44522 -- -3.0 19.76
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)
1.85 1.9 99.9 0.508 -- 2.12 -- --

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 1.85 41.206 -- 1.36 -- 44462 2167 99.68 -- 0.179 0.1772 0.2126 --
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 1.85 1.8931 -- 139 2821 0.2668 0.2921 -- 100.0
X Ray Diffraction 1.8931 1.9404 -- 126 2760 0.2411 0.3032 -- 100.0
X Ray Diffraction 1.9404 1.9929 -- 139 2790 0.2082 0.2825 -- 100.0
X Ray Diffraction 1.9929 2.0515 -- 145 2766 0.2033 0.2452 -- 100.0
X Ray Diffraction 2.0515 2.1177 -- 158 2780 0.2068 0.2288 -- 100.0
X Ray Diffraction 2.1177 2.1934 -- 145 2774 0.1916 0.2578 -- 99.0
X Ray Diffraction 2.1934 2.2812 -- 150 2747 0.1874 0.2189 -- 99.0
X Ray Diffraction 2.2812 2.385 -- 160 2797 0.1788 0.22 -- 99.0
X Ray Diffraction 2.385 2.5107 -- 149 2796 0.1771 0.2152 -- 99.0
X Ray Diffraction 2.5107 2.668 -- 134 2797 0.17 0.2245 -- 99.0
X Ray Diffraction 2.668 2.874 -- 143 2810 0.179 0.224 -- 99.0
X Ray Diffraction 2.874 3.1631 -- 156 2826 0.1761 0.1948 -- 100.0
X Ray Diffraction 3.1631 3.6206 -- 122 2870 0.1618 0.1862 -- 100.0
X Ray Diffraction 3.6206 4.5606 -- 135 2915 0.1475 0.1955 -- 100.0
X Ray Diffraction 4.5606 41.2167 -- 166 3046 0.1657 0.174 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.4035
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.031
f_dihedral_angle_d 12.852
f_angle_d 0.876
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3904
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 483

Software

Software
Software Name Purpose
XDS data reduction
PHENIX refinement version: (phenix.refine: 1.9_1675)
PDB_EXTRACT data extraction version: 3.15
XSCALE data scaling