X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 293.0
Details PEG 4000, DMSO, sodium chloride, sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.05 α = 90
b = 102.05 β = 90
c = 35.28 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2001-01-01
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL40B2 0.977 SPRING-8 BL40B2

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
2.6 50 98.2 0.05 -- -- -- 31746 32025 -- -- --
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)
2.6 2.69 89.0 0.206 -- -- -- 597

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
-- 2.6 18.73 -- 1.0 6521 6648 646 98.09 0.23376 0.23376 0.2287 0.2822 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 2.601 2.667 -- 35 360 0.298 0.361 -- 98.09
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.481
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] -0.01
Anisotropic B[2][2] -0.01
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.341
r_gen_planes_refined 0.007
r_chiral_restr 0.156
r_dihedral_angle_3_deg 19.733
r_dihedral_angle_1_deg 4.471
r_angle_refined_deg 2.116
r_bond_refined_d 0.024
r_xyhbond_nbd_refined 0.215
r_symmetry_vdw_refined 0.419
r_symmetry_hbond_refined 0.787
r_mcbond_it 4.304
r_mcangle_it 7.736
r_scbond_it 11.219
r_scangle_it 13.342
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1388
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 15

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
EPMR model building
SCALEPACK data reduction
DENZO data collection