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 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_scangle_it 2.744
r_scbond_it 1.636
r_mcangle_it 1.056
r_mcbond_it 0.593
r_nbd_refined 0.207
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.077
r_dihedral_angle_4_deg 15.238
r_dihedral_angle_3_deg 14.729
r_dihedral_angle_2_deg 33.334
r_dihedral_angle_1_deg 6.281
r_angle_other_deg 0.792
r_angle_refined_deg 1.451
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_nbd_other 0.178
r_nbtor_refined 0.184
r_nbtor_other 0.084
r_xyhbond_nbd_refined 0.153
r_symmetry_vdw_refined 0.158
r_symmetry_vdw_other 0.264
r_symmetry_hbond_refined 0.171
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

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