X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details 0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.89 α = 90
b = 97.89 β = 90
c = 80.49 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2005-01-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FRE -- -- --

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
2.45 50 99.8 0.1 -- -- 7.33 -- 16216 -- 3.0 --
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)
2.45 2.55 99.0 0.55 -- 3.28 6.24 --

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 2.45 42.0 -- -- -- 15369 814 99.8 -- 0.191 0.189 0.225 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 2.45 2.51 -- 62 1120 0.33 0.354 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.89
Anisotropic B[1][1] 2.43
Anisotropic B[1][2] 1.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.64
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.077
r_symmetry_vdw_other 0.264
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 15.238
r_symmetry_vdw_refined 0.158
r_nbd_other 0.178
r_mcangle_it 1.056
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.153
r_nbtor_refined 0.184
r_angle_other_deg 0.792
r_nbd_refined 0.207
r_scbond_it 1.636
r_dihedral_angle_3_deg 14.729
r_scangle_it 2.744
r_dihedral_angle_2_deg 33.334
r_bond_refined_d 0.013
r_dihedral_angle_1_deg 6.281
r_angle_refined_deg 1.451
r_symmetry_hbond_refined 0.171
r_mcbond_it 0.593
r_nbtor_other 0.084
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2223
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 23

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
DENZO data reduction
SCALEPACK data scaling
PHASER phasing