X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.2M Sodium chloride, 0.1M Na/K phosphate pH 6.5, 25% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.34 α = 90
b = 138.14 β = 127.89
c = 64.46 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2012-06-18
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 3W1A 0.9793 BSRF 3W1A

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
2.1 50 100.0 0.062 -- -- 7.7 36726 36726 0.0 0.0 --
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)
2.1 2.14 100.0 0.232 -- 10.5 7.5 1834

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 2.1 23.402 -- 1.35 36681 36681 1834 99.96 0.1591 0.1568 0.1568 0.2035 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 2.1 2.1568 -- 138 2675 0.1745 0.2455 -- 100.0
X Ray Diffraction 2.1568 2.2202 -- 163 2645 0.1502 0.2132 -- 100.0
X Ray Diffraction 2.2202 2.2918 -- 124 2678 0.1426 0.2166 -- 100.0
X Ray Diffraction 2.2918 2.3736 -- 144 2679 0.1442 0.2031 -- 100.0
X Ray Diffraction 2.3736 2.4685 -- 129 2695 0.1514 0.2161 -- 100.0
X Ray Diffraction 2.4685 2.5808 -- 136 2678 0.1517 0.2214 -- 100.0
X Ray Diffraction 2.5808 2.7166 -- 136 2666 0.1591 0.2229 -- 100.0
X Ray Diffraction 2.7166 2.8866 -- 152 2683 0.1588 0.1901 -- 100.0
X Ray Diffraction 2.8866 3.109 -- 126 2681 0.1612 0.207 -- 100.0
X Ray Diffraction 3.109 3.421 -- 140 2693 0.1663 0.2104 -- 100.0
X Ray Diffraction 3.421 3.914 -- 146 2688 0.1546 0.1916 -- 100.0
X Ray Diffraction 3.914 4.9236 -- 146 2676 0.135 0.1673 -- 100.0
X Ray Diffraction 4.9236 23.4039 -- 154 2710 0.186 0.2102 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.7697
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.0899
Anisotropic B[2][2] -2.4582
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.6885
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.071
f_dihedral_angle_d 12.595
f_angle_d 1.057
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3934
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 477

Software

Computing
Computing Package Purpose
marccd Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
marccd data collection