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 = 98.28 α = 90
b = 98.28 β = 90
c = 80.64 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 -- 2011-01-24
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 BL26B2 1.0 SPring-8 BL26B2

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
2.08 32.17 99.7 0.078 0.078 -- 6.4 26602 26602 -- -- 29.1
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)
2.08 2.19 100.0 0.391 0.391 2.0 6.4 3888

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 2.08 32.17 -- 0.0 -- 26602 1346 99.77 -- 0.1749 0.1735 0.2003 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 2.08 2.134 1843 96 1843 0.202 0.218 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.2034
Anisotropic B[1][1] 0.63
Anisotropic B[1][2] 0.32
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.95
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.226
r_angle_refined_deg 1.506
r_bond_refined_d 0.013
r_dihedral_angle_4_deg 16.623
r_scangle_it 3.679
r_dihedral_angle_1_deg 5.5
r_chiral_restr 0.089
r_mcangle_it 1.591
r_dihedral_angle_2_deg 33.036
r_gen_planes_refined 0.006
r_mcbond_it 0.828
r_dihedral_angle_3_deg 13.182
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2131
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 237

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
MOSFLM data reduction