X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 50mM HEPES at pH 7.0, 4.0M lithium chloride, 5%(v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.72 α = 90
b = 63.72 β = 90
c = 114.02 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97925, 0.97942, 0.95000 Photon Factory BL-5A

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
1.5 20 -- -- -- -- -- -- 38216 -- -- --

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
MAD 1.5 20.0 -- -- -- 34377 3806 99.55 -- 0.18701 0.18464 0.20823 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 1.5 1.539 -- 299 2438 0.221 0.241 -- 99.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.951
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.079
r_dihedral_angle_4_deg 14.528
r_scbond_it 1.906
r_bond_refined_d 0.008
r_nbtor_refined 0.313
r_mcangle_it 1.196
r_dihedral_angle_1_deg 5.868
r_dihedral_angle_2_deg 35.075
r_nbd_refined 0.191
r_xyhbond_nbd_refined 0.112
r_gen_planes_refined 0.005
r_scangle_it 3.066
r_mcbond_it 0.768
r_symmetry_hbond_refined 0.146
r_symmetry_vdw_refined 0.235
r_angle_refined_deg 1.209
r_dihedral_angle_3_deg 11.566
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1643
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 380

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
SOLVE phasing