X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details 3.1 M Na Formate, 0.1 M Tris pH 8, 5 mM AMP, 5 mM MgCL2, 1 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.77 α = 90
b = 140.74 β = 90
c = 60.4 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2012-02-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178 -- --

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 50 99.8 -- 0.124 -- 7.1 63013 62887 0.0 0.0 --
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)
2.0 2.03 96.4 -- 0.626 3.15 6.7 2993

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 2.0 35.0 -- 0.0 62864 62607 3179 99.59 0.1508 0.1508 0.1487 0.191 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 2.0 2.052 -- 247 4258 0.211 0.264 -- 98.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.7924
Anisotropic B[1][1] 0.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_bond_other_d 0.001
r_gen_planes_refined 0.006
r_angle_refined_deg 1.299
r_dihedral_angle_4_deg 15.884
r_bond_refined_d 0.011
r_mcbond_other 0.132
r_scangle_it 2.682
r_mcbond_it 0.524
r_chiral_restr 0.075
r_dihedral_angle_1_deg 5.399
r_dihedral_angle_3_deg 13.871
r_dihedral_angle_2_deg 36.721
r_mcangle_it 0.964
r_scbond_it 1.65
r_angle_other_deg 0.913
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7154
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 709

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
rigaku data collection
HKL data reduction
HKL data scaling
PHASER phasing