X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 1.2 M sodium citrate, 0.1 M HEPES-NaOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.55 α = 90
b = 87.55 β = 90
c = 131.88 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-01-17
Diffraction Radiation
Monochromator Protocol
Numerical link type Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A

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
1.8 75.8 98.3 -- -- -- -- 104764 102983 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)
1.8 1.9 97.4 -- -- -- -- --

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 1.8 65.82 -- 0.0 99532 97850 5130 98.31 -- 0.16532 0.16398 0.19052 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 1.8 1.847 -- 365 7100 0.229 0.277 -- 97.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.7
Anisotropic B[1][1] -0.86
Anisotropic B[1][2] -0.86
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.79
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.134
r_bond_refined_d 0.022
r_angle_other_deg 0.983
r_angle_refined_deg 1.719
r_gen_planes_other 0.001
r_gen_planes_refined 0.01
r_dihedral_angle_1_deg 5.382
r_bond_other_d 0.005
r_dihedral_angle_2_deg 37.195
r_dihedral_angle_3_deg 13.801
r_dihedral_angle_4_deg 25.912
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6986
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 934

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
MOLREP phasing
REFMAC refinement version: 5.7.0029
MOSFLM data reduction
SCALA data scaling