X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 277.0
Details 2.0-2.2 M K/Na phosphate, pH 6.9, 5mM BME and 5mM oxidized BME. Complexes were prepared by soaking or vapor diffusion methods, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.03 α = 90
b = 60.03 β = 90
c = 95.96 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2005-03-25
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.542 -- --

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
1.8 53 98.2 -- -- -- -- -- 18504 2.0 2.0 --
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)
1.8 1.86 96.4 -- -- -- -- --

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 1.8 45.69 -- -- -- 17524 945 97.83 -- 0.18578 0.18383 0.22143 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 1.8 1.848 -- 58 989 0.283 0.418 -- 90.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.442
Anisotropic B[1][1] 0.04
Anisotropic B[1][2] 0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 14.993
r_bond_refined_d 0.009
r_nbd_refined 0.198
r_symmetry_vdw_refined 0.157
r_scangle_it 1.975
r_angle_refined_deg 0.974
r_dihedral_angle_1_deg 4.772
r_dihedral_angle_2_deg 31.503
r_chiral_restr 0.062
r_dihedral_angle_3_deg 12.428
r_mcangle_it 0.811
r_mcbond_it 0.506
r_xyhbond_nbd_refined 0.106
r_scbond_it 1.255
r_nbtor_refined 0.291
r_gen_planes_refined 0.003
r_symmetry_hbond_refined 0.059
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1328
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 245

Software

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