X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 38-40% pentaerythritol propoxylate (5/4 PO/OH), 50mM Tris-HCl, 200mM KCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.56 α = 90
b = 106.4 β = 96.5
c = 82.78 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 RIGAKU JUPITER 210 -- 2006-06-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1

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 50 97.2 0.078 -- -- 1.9 -- 70989 -- -- --
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)
2.0 2.07 93.2 0.377 -- 2.34 1.8 4546

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 2.0 19.94 -- -- -- 64876 3452 97.19 -- 0.18514 0.18337 0.21851 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 2.0 2.051 -- 238 4546 0.232 0.259 -- 92.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.587
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.336
r_scbond_it 0.748
r_mcangle_it 0.578
r_scangle_it 1.244
r_dihedral_angle_4_deg 10.364
r_gen_planes_refined 0.002
r_xyhbond_nbd_refined 0.093
r_nbtor_refined 0.298
r_symmetry_vdw_refined 0.141
r_chiral_restr 0.066
r_dihedral_angle_2_deg 36.232
r_nbd_refined 0.173
r_angle_refined_deg 0.933
r_symmetry_hbond_refined 0.096
r_bond_refined_d 0.006
r_dihedral_angle_1_deg 5.046
r_dihedral_angle_3_deg 11.95
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7460
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 820

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing