X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 298.0
Details 0.1M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.92 α = 90
b = 88.92 β = 90
c = 236.22 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-06-16
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.979 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
1.84 50 99.5 0.116 0.079 -- 23.8 82827 82827 -- -- 22.4
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)
1.84 1.87 90.2 0.97 0.895 3.875 22.4 3700

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
AB INITIO PHASING 1.84 43.69 -- 0.0 82357 82357 4129 99.47 -- 0.1647 0.1629 0.1997 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 1.842 1.89 -- 275 5625 0.226 0.256 -- 98.32
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.0755
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_gen_planes_refined 0.014
r_chiral_restr 0.085
r_dihedral_angle_4_deg 14.455
r_dihedral_angle_3_deg 13.359
r_dihedral_angle_2_deg 36.0
r_dihedral_angle_1_deg 5.877
r_angle_other_deg 0.695
r_angle_refined_deg 1.433
r_bond_other_d 0.0
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6824
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 528

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Arp/Warp, hkl2map, PHENIX Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction