X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details AMMONIUM SULPHATE 1.4M, 2-PROPANOL 5-7%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.56 α = 90
b = 73.35 β = 90
c = 95.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 mirrors 2011-02-07
Diffraction Radiation
Monochromator Protocol
Numerical link type Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 PHOTON FACTORY AR-NW12A

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
1.5 58.18 98.2 0.058 -- -- 6.9 41000 40264 0.0 -3.0 --
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)
1.5 1.55 84.0 0.49 -- 2.7 4.8 3395

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 1.5 50.0 -- 0.0 41000 40065 1605 97.72 0.1523 0.1523 0.1503 0.2017 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 1.499 1.538 -- 89 2232 0.202 0.262 -- 81.18
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.8173
Anisotropic B[1][1] 2.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.02
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 15.258
r_sphericity_free 30.884
r_rigid_bond_restr 4.607
r_gen_planes_refined 0.009
r_chiral_restr 0.117
r_dihedral_angle_4_deg 16.594
r_dihedral_angle_3_deg 13.795
r_dihedral_angle_2_deg 34.092
r_dihedral_angle_1_deg 5.695
r_angle_refined_deg 1.583
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1920
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 250

Software

Computing
Computing Package Purpose
UGUI Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 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: 2.1.4 molecular replacement
HKL data reduction