X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details Lithium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.29 α = 90
b = 97.29 β = 90
c = 46.91 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2004-11-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.3 84.51 99.7 0.093 -- -- -- 11460 11417 1.0 1.0 --
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)
2.3 2.38 97.9 0.451 -- -- -- --

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 2.3 30.0 -- 2.0 11460 10842 548 99.56 0.207 0.207 0.203 0.28 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 2.3 2.36 -- 32 795 0.327 0.324 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.345
Anisotropic B[1][1] -4.82
Anisotropic B[1][2] -2.41
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.23
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.626
r_symmetry_vdw_refined 0.254
r_bond_refined_d 0.042
r_angle_refined_deg 3.25
r_gen_planes_refined 0.015
r_chiral_restr 0.243
r_dihedral_angle_1_deg 10.268
r_xyhbond_nbd_refined 0.213
r_scangle_it 8.113
r_mcangle_it 3.018
r_scbond_it 5.479
r_nbd_refined 0.299
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1261
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 66

Software

Software
Software Name Purpose
HKL data processing
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 1.601
DENZO data reduction
SCALEPACK data scaling