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 = 98.21 α = 90
b = 98.21 β = 90
c = 80.88 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 MX225HE -- 2009-06-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU

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
2.55 85.13 99.4 0.074 0.074 -- 5.8 14489 14489 -- -- 54.31
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)
2.55 2.69 98.9 0.404 0.404 1.9 5.8 2099

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 2.55 85.126 -- 0.0 -- 14485 714 99.43 -- 0.1798 0.1773 0.2288 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 2.55 2.616 1018 51 1018 0.24 0.318 -- 98.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.2663
Anisotropic B[1][1] 0.92
Anisotropic B[1][2] 0.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.38
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.066
r_dihedral_angle_1_deg 6.432
r_mcangle_it 2.073
r_dihedral_angle_2_deg 34.036
r_dihedral_angle_4_deg 19.079
r_gen_planes_refined 0.008
r_bond_refined_d 0.02
r_chiral_restr 0.119
r_scbond_it 3.032
r_mcbond_it 1.07
r_angle_refined_deg 1.993
r_dihedral_angle_3_deg 15.975
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2099
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 112

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