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
1.7 53 99.6 -- -- -- -- -- 22609 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)
1.7 1.76 100.0 -- -- -- -- --

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 1.7 21.89 -- -- -- 21144 1144 99.67 -- 0.19773 0.19635 0.22297 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 1.7 1.744 -- 78 1317 0.262 0.371 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.219
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.26
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 11.268
r_scangle_it 2.115
r_dihedral_angle_1_deg 4.476
r_angle_refined_deg 0.945
r_gen_planes_refined 0.003
r_mcbond_it 0.455
r_symmetry_vdw_refined 0.224
r_nbd_refined 0.188
r_bond_refined_d 0.007
r_chiral_restr 0.063
r_mcangle_it 0.788
r_dihedral_angle_4_deg 15.23
r_xyhbond_nbd_refined 0.092
r_symmetry_hbond_refined 0.168
r_nbtor_refined 0.296
r_scbond_it 1.302
r_dihedral_angle_2_deg 32.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1304
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 210

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