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_scangle_it 2.682
r_scbond_it 1.65
r_mcangle_it 0.964
r_mcbond_other 0.132
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.299
r_angle_other_deg 0.913
r_dihedral_angle_1_deg 5.399
r_dihedral_angle_2_deg 36.721
r_dihedral_angle_3_deg 13.871
r_dihedral_angle_4_deg 15.884
r_chiral_restr 0.075
r_gen_planes_refined 0.006
r_gen_planes_other 0.002
r_mcbond_it 0.524
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

Computing
Computing Package Purpose
rigaku Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement