X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 277.0
Details 12% PEG 8,000, 15 mM CoCl2, 200 mM NaCl, and 100 mM MES 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.25 α = 90
b = 60.25 β = 90
c = 345.57 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 KB Bimorph Mirrors 2010-10-13
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D

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
2.7 30 64.0 -- 0.065 -- 4.0 12037 11782 -- -3.0 --
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)
2.7 2.75 21.4 -- 0.441 1.6 2.7 189

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 2.71 29.98 -- -- 11078 11078 572 63.29 0.19298 0.19298 0.1901 0.2516 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 2.71 2.782 -- 9 199 0.333 0.37 -- 16.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 96.352
Anisotropic B[1][1] -0.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.056
r_dihedral_angle_4_deg 14.809
r_dihedral_angle_3_deg 17.086
r_dihedral_angle_2_deg 39.875
r_dihedral_angle_1_deg 5.805
r_angle_other_deg 0.801
r_angle_refined_deg 1.118
r_bond_other_d 0.001
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3696
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 16

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASER model building