X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 22% PEG 400, 0.2M CaCl2, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 155.39 α = 90
b = 155.39 β = 90
c = 317.85 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2011-09-25
Diffraction Radiation
Monochromator Protocol
Varimax optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
3.19 29.74 99.6 0.315 -- -- -- -- 38297 -- -3.0 17.228
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)
3.19 3.39 99.0 0.733 -- 5.35 -- --

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 3.19 29.74 -- 0.0 -- 38297 1915 100.0 -- 0.2059 0.2022 0.277 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 3.194 3.276 -- 135 2563 0.244 0.37 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.828
Anisotropic B[1][1] -1.77
Anisotropic B[1][2] -0.88
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.65
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 39.934
r_angle_refined_deg 0.995
r_mcbond_it 0.163
r_dihedral_angle_4_deg 19.342
r_mcangle_it 0.291
r_scbond_it 0.057
r_scangle_it 0.122
r_dihedral_angle_3_deg 15.637
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 5.018
r_bond_refined_d 0.006
r_chiral_restr 0.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14999
Nucleic Acid Atoms 0
Heterogen Atoms 308
Solvent Atoms 414

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
XDS data reduction
XDS data scaling