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_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.092
r_dihedral_angle_4_deg 16.03
r_dihedral_angle_3_deg 12.975
r_dihedral_angle_2_deg 31.077
r_dihedral_angle_1_deg 6.036
r_angle_other_deg 0.993
r_angle_refined_deg 1.597
r_bond_other_d 0.001
r_bond_refined_d 0.014
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

Computing
Computing Package Purpose
StructureStudio Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.3.0 molecular replacement
Xscale data reduction