X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.15
Details 20% PEG 3350, 0.2 M Na/K tartrate, 0.1 M Bis-Tris propane, pH 6.5, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.54 α = 90
b = 86.54 β = 90
c = 226.92 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2012-04-21
Diffraction Radiation
Monochromator Protocol
Si (111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9778 Diamond I03

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
2.05 86.6 99.5 0.084 -- -- 3.2 103494 103422 0.0 0.0 26.7
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)
2.049 2.16 97.1 0.422 -- 2.1 2.5 14756

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 2.049 86.55 2.0 0.0 103422 98138 5283 99.3 0.228 0.14995 0.14793 0.18753 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 2.049 2.102 -- 375 6891 0.202 0.275 -- 94.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.418
Anisotropic B[1][1] 6.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.43
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_dihedral_angle_4_deg 18.778
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 6.644
r_dihedral_angle_3_deg 13.864
r_chiral_restr 0.091
r_bond_other_d 0.003
r_bond_refined_d 0.015
r_angle_other_deg 1.012
r_angle_refined_deg 1.576
r_dihedral_angle_2_deg 35.758
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.258
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11732
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 865

Software

Software
Software Name Purpose
GDA data collection
PHASER phasing
REFMAC refinement version: 5.6.0117
MOSFLM data reduction
SCALA data scaling