X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 20% (w/v) PEG-1000, 0.1 M imidazole pH 8.0, 0.2 M calcium acetate, 100 mM tribasic sodium citrate, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.89 α = 90
b = 39.89 β = 90
c = 82.12 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR RIGAKU RAXIS HTC -- 2010-11-01
Diffraction Radiation
Monochromator Protocol
CONFOCAL MIRRORS Varimax HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
1.9 80 98.99 -- 0.1 -- 11.5 5691 5640 -- -- 33.21
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)
1.9 1.97 -- -- 0.459 3.38 6.6 --

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 1.9 35.882 -- 0.0 -- 5593 560 98.99 -- 0.2088 0.2068 0.228 --
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 1.9002 2.0914 -- 136 1223 0.2427 0.265 -- 100.0
X Ray Diffraction 2.0914 2.394 -- 137 1231 0.1852 0.2502 -- 100.0
X Ray Diffraction 2.394 3.016 -- 141 1259 0.2045 0.2311 -- 100.0
X Ray Diffraction 3.016 35.8884 -- 146 1320 0.2075 0.2169 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.9949
Anisotropic B[1][1] 6.2576
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.2576
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.5151
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.561
f_plane_restr 0.005
f_chiral_restr 0.069
f_angle_d 1.109
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 450
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 27

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
DENZO data collection