X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 289.0
Details 16% PEG 3350, 0.2 M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.82 α = 90
b = 50.94 β = 103.48
c = 65.02 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
-- -- -- 2011-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
1.23 50 95.5 0.06 -- -- 3.4 -- 77799 -- -- --
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)
1.23 1.25 83.5 0.998 -- -- 3.2 --

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
SAD 1.23 32.04 -- 0.0 -- 77765 7794 95.3 -- 0.152 0.15 0.17 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 1.23 1.26 -- 420 4519 0.255 0.28 -- 83.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.47
Anisotropic B[1][1] -0.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.09
Anisotropic B[2][2] -0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.97
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 8.745
r_sphericity_free 22.098
r_rigid_bond_restr 14.281
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.084
r_dihedral_angle_4_deg 12.293
r_dihedral_angle_3_deg 10.859
r_dihedral_angle_2_deg 30.882
r_dihedral_angle_1_deg 5.574
r_angle_other_deg 0.843
r_angle_refined_deg 1.8
r_bond_other_d 0.001
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2181
Nucleic Acid Atoms 0
Heterogen Atoms 126
Solvent Atoms 422

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SCALEPACK data reduction