X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 9.5
Temperature 291.0
Details 1.9 M (NH4)H2PO4, 0.1 M bis-tris propane, pH 9.5, 2.5% glycerol, vapor diffusion, temperature 291K, VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 183.64 α = 90
b = 183.64 β = 90
c = 45.21 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM Q315r -- 2008-09-27
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) or Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29

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
2.59 45.22 99.7 0.086 0.086 -- 13.2 14430 14430 0.0 0.0 64.8
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)
2.59 2.73 98.4 0.758 0.758 3.8 13.0 2020

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 2.6 45.0 -- 0.0 14341 14341 722 99.97 0.226 0.226 0.224 0.254 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 2.6 2.668 -- 45 994 0.341 0.456 -- 99.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.103
Anisotropic B[1][1] -1.06
Anisotropic B[1][2] -0.53
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.58
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.07
r_dihedral_angle_1_deg 5.639
r_symmetry_hbond_refined 0.121
r_mcbond_it 0.458
r_bond_refined_d 0.009
r_mcangle_it 0.817
r_gen_planes_refined 0.003
r_scbond_it 0.966
r_scangle_it 1.609
r_angle_refined_deg 1.362
r_dihedral_angle_4_deg 17.41
r_nbd_refined 0.211
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.123
r_symmetry_vdw_refined 0.152
r_dihedral_angle_2_deg 34.896
r_dihedral_angle_3_deg 18.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2003
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 38

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
ADSC data collection version: Quantum
XDS data reduction
SCALA data scaling