X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5
Temperature 298.0
Details 12 % PEG 3350, 0.25 M ammonium acetate, 50 mM sodium acetate, pH 5.0, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 154.37 α = 90
b = 139.12 β = 90.02
c = 175.32 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
CCD ADSC QUANTUM 210 -- 2006-11-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F2 0.97950 CHESS F2

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
2.57 50 99.8 0.097 -- -- 3.8 231454 231454 1.0 1.0 53.0
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)
2.57 2.69 99.0 0.456 -- 2.4 3.3 22862

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 2.58 43.07 -- 0.0 233995 231396 11664 98.89 0.23 0.23 0.227 0.291 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 2.58 2.642 14714 773 13941 0.32 0.417 -- 85.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.071
Anisotropic B[1][1] -0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.04
Anisotropic B[2][2] 0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 17.2
r_dihedral_angle_2_deg 36.399
r_gen_planes_refined 0.004
r_mcangle_it 0.757
r_xyhbond_nbd_refined 0.148
r_nbtor_refined 0.303
r_symmetry_vdw_refined 0.145
r_dihedral_angle_1_deg 6.707
r_dihedral_angle_4_deg 19.334
r_nbd_refined 0.208
r_scbond_it 1.193
r_mcbond_it 0.424
r_angle_refined_deg 1.439
r_chiral_restr 0.093
r_symmetry_hbond_refined 0.111
r_bond_refined_d 0.012
r_scangle_it 1.987
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 37083
Nucleic Acid Atoms 0
Heterogen Atoms 916
Solvent Atoms 1036

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
DM phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.000
ADSC data collection version: Quantum