X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details ButhA.01187.a.A1 PS01190 at 25 mg/mL against Morpheus screen condition H4, 0.1 M MES/immidazole, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02 M L-glutamate, alanine, lysine, serine, glycine, crystal tracking ID 233960h4, unique puck ID xgv5-8, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.95 α = 90
b = 88.95 β = 90
c = 132.27 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-07-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1

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
2.05 50 100.0 0.065 -- -- 9.5 34021 34013 -- -- --
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)
2.05 2.1 100.0 0.505 -- 4.69 9.2 2455

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 2.05 45.62 -- 0.0 -- 34012 1725 99.96 -- 0.2012 0.1993 0.2375 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 2.05 2.103 -- 130 2316 0.22 0.265 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.6175
Anisotropic B[1][1] 0.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.07
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 34.148
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_other_deg 0.817
r_dihedral_angle_3_deg 12.963
r_dihedral_angle_1_deg 5.572
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 17.998
r_angle_refined_deg 1.427
r_chiral_restr 0.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2942
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 200

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
REFMAC refinement version: 5.7.0029
PDB_EXTRACT data extraction version: 3.11
XDS data reduction