X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 290.0
Details EmeraldBio PACT screen e12: 20% PEG 3350, 200mM NaMalonate pH 7.0, LemaA.01471.b.B1.PS00838 at 19mg/ml with 2.5mM PLP, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.41 α = 90
b = 93.67 β = 106.57
c = 74.59 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ RIGAKU VARIMAX 2012-05-22
Diffraction Radiation
Monochromator Protocol
RIGAKU VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
1.85 50 99.6 0.054 -- -- 5.2 69108 68837 0.0 -3.0 25.426
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)
1.85 1.9 98.7 0.541 -- 2.26 -- 5102

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 1.85 50.0 -- 0.0 -- 68814 3471 99.69 -- 0.1698 0.1675 0.2129 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 1.85 1.898 -- 244 4697 0.274 0.307 -- 98.72
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.923
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.28
Anisotropic B[2][2] -0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.27
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.597
r_dihedral_angle_4_deg 16.03
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_angle_other_deg 0.993
r_dihedral_angle_3_deg 12.975
r_bond_other_d 0.001
r_dihedral_angle_2_deg 31.077
r_chiral_restr 0.092
r_bond_refined_d 0.014
r_dihedral_angle_1_deg 6.036
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6221
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 757

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.3.0
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
StructureStudio data collection
XDS data reduction