X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 100mM CITRATE BUFFER PH 5.5, 200mM NACL, 1M NH4HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.01 α = 90
b = 97.01 β = 90
c = 80.9 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2009-04-20
Diffraction Radiation
Monochromator Protocol
FIXED EXIT SI DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0 SPring-8 BL32B2

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
2.2 29.14 100.0 0.083 0.083 -- 22.8 -- 22062 -- -- 34.61
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)
2.2 2.32 100.0 0.427 0.427 1.8 22.7 3189

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 2.2 29.14 -- 0.0 -- 20930 1102 99.99 -- 0.1682 0.1664 0.2011 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 2.2 2.257 1540 84 1540 0.177 0.208 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.7977
Anisotropic B[1][1] 0.86
Anisotropic B[1][2] 0.43
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.3
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 34.174
r_dihedral_angle_3_deg 13.041
r_dihedral_angle_4_deg 16.469
r_gen_planes_refined 0.006
r_scbond_it 2.406
r_angle_refined_deg 1.294
r_mcbond_it 0.861
r_dihedral_angle_1_deg 5.666
r_chiral_restr 0.096
r_mcangle_it 1.661
r_bond_refined_d 0.014
r_scangle_it 3.917
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2168
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 241

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
PHASER phasing version: 2.1.2
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
MOSFLM data reduction