X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 292.0
Details 20% PEG 3350, 1.0 M LiCl, 0.1M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.63 α = 90
b = 121.63 β = 90
c = 157.21 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2002-11-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1

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
3 30 99.6 -- 0.081 -- 3.5 26356 26356 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)
3.0 3.11 98.8 -- 0.41 2.5 3.5 2630

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 3.0 30.0 -3.0 0.0 -- 23768 2536 99.57 -- 0.21992 0.21288 0.28633 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 3.0 3.078 -- 308 1609 0.24 0.364 -- 98.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.339
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.1
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.29
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.077
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 6.766
r_angle_other_deg 0.775
r_symmetry_vdw_other 0.261
r_scangle_it 1.722
r_symmetry_vdw_refined 0.109
r_scbond_it 1.042
r_angle_refined_deg 1.357
r_bond_other_d 0.002
r_bond_refined_d 0.012
r_nbtor_other 0.088
r_gen_planes_refined 0.004
r_nbd_other 0.234
r_xyhbond_nbd_refined 0.154
r_mcbond_it 0.931
r_symmetry_hbond_refined 0.023
r_mcangle_it 1.678
r_nbd_refined 0.197
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7507
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 20

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing