X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 291.0
Details Wild type AbyA5 data sets were collected from crystals formed in formed in 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, HCl, 0.02 M DL-serine, 0.1 M Bicine/Trizma base pH 8.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.23 α = 90
b = 88.36 β = 90
c = 131.29 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 65
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2013-08-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 0.97887 Diamond I24

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
2.5 41.93 96.6 -- -- -- 11.8 -- 27564 -- -- --
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)
-- -- -- -- -- -- -- --

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 2.5 73.3 -- -- -- 26076 1356 96.01 -- 0.21079 0.20812 0.2608 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 2.5 2.565 -- 106 1898 0.248 0.263 -- 95.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.384
Anisotropic B[1][1] -2.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.14
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.015
r_long_range_B_other 3.049
r_angle_refined_deg 1.714
r_scbond_other 1.285
r_mcbond_other 0.903
r_scbond_it 1.285
r_mcbond_it 0.903
r_dihedral_angle_4_deg 19.304
r_long_range_B_refined 3.057
r_dihedral_angle_1_deg 6.224
r_dihedral_angle_3_deg 15.43
r_mcangle_it 1.502
r_bond_other_d 0.002
r_mcangle_other 1.502
r_dihedral_angle_2_deg 30.423
r_chiral_restr 0.096
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_scangle_other 2.123
r_angle_other_deg 1.081
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5301
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 98

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
iMOSFLM data reduction
SCALA data scaling
PHASER phasing