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 = 97.53 α = 90
b = 97.53 β = 90
c = 80.73 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 2005-03-04
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
1.9 50 99.6 0.06 -- -- 5.55 -- 34487 -- 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)
1.9 2.0 97.8 0.33 -- 3.25 3.69 --

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 1.9 40.0 -- -- -- 32701 1751 99.7 -- 0.159 0.157 0.19 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 1.9 1.95 -- 140 2363 0.24 0.303 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.2
Anisotropic B[1][1] 0.4
Anisotropic B[1][2] 0.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.6
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.213
r_xyhbond_nbd_refined 0.122
r_scangle_it 6.05
r_angle_refined_deg 1.279
r_scbond_it 4.084
r_symmetry_hbond_refined 0.176
r_symmetry_vdw_other 0.31
r_nbtor_other 0.079
r_dihedral_angle_4_deg 17.879
r_nbtor_refined 0.182
r_bond_refined_d 0.012
r_bond_other_d 0.001
r_angle_other_deg 0.827
r_dihedral_angle_3_deg 12.026
r_symmetry_vdw_refined 0.043
r_gen_planes_refined 0.006
r_mcangle_it 2.933
r_dihedral_angle_2_deg 33.947
r_chiral_restr 0.087
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 5.449
r_nbd_other 0.183
r_mcbond_it 1.952
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2204
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 232

Software

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