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 = 98.24 α = 90
b = 98.24 β = 90
c = 80.89 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 MARRESEARCH MIRRORS 2005-03-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 -- BESSY 14.2

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 97.1 0.04 -- -- 5.1 -- 34129 -- 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 97.0 0.24 -- 3.4 2.9 --

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 -- -- -- 31653 1709 95.1 -- 0.218 0.216 0.265 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 -- 114 1799 0.626 0.694 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.54
Anisotropic B[1][1] 0.42
Anisotropic B[1][2] 0.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.081
r_scbond_it 3.233
r_mcangle_it 2.132
r_mcbond_it 1.27
r_nbd_refined 0.196
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.07
r_dihedral_angle_4_deg 15.212
r_dihedral_angle_3_deg 13.005
r_dihedral_angle_2_deg 35.331
r_dihedral_angle_1_deg 5.489
r_angle_other_deg 0.77
r_angle_refined_deg 1.106
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_nbd_other 0.172
r_nbtor_refined 0.178
r_nbtor_other 0.081
r_xyhbond_nbd_refined 0.161
r_symmetry_vdw_refined 0.272
r_symmetry_vdw_other 0.264
r_symmetry_hbond_refined 0.175
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2214
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 268

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