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 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_scangle_it 6.05
r_scbond_it 4.084
r_mcangle_it 2.933
r_mcbond_it 1.952
r_nbd_refined 0.213
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.087
r_dihedral_angle_4_deg 17.879
r_dihedral_angle_3_deg 12.026
r_dihedral_angle_2_deg 33.947
r_dihedral_angle_1_deg 5.449
r_angle_other_deg 0.827
r_angle_refined_deg 1.279
r_bond_other_d 0.001
r_bond_refined_d 0.012
r_nbd_other 0.183
r_nbtor_refined 0.182
r_nbtor_other 0.079
r_xyhbond_nbd_refined 0.122
r_symmetry_vdw_refined 0.043
r_symmetry_vdw_other 0.31
r_symmetry_hbond_refined 0.176
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
PHASER model building