X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 2.25 M Lithium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.89 α = 90
b = 115.89 β = 90
c = 108.15 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 -- 2002-03-01
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
1.9 30 -- 0.059 -- -- 2.7 64839 64839 -- -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)
1.9 1.97 96.8 0.469 -- 2.5 2.7 --

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 1.9 26.13 -- -- 64834 60113 3227 97.74 -- 0.19327 0.19189 0.21916 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 1.9 1.949 -- 235 4332 0.275 0.296 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.424
Anisotropic B[1][1] 0.38
Anisotropic B[1][2] 0.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.566
r_symmetry_hbond_refined 0.211
r_chiral_restr 0.102
r_dihedral_angle_2_deg 17.811
r_symmetry_vdw_refined 0.263
r_nbd_refined 0.239
r_xyhbond_nbd_refined 0.137
r_mcbond_it 1.366
r_dihedral_angle_1_deg 4.137
r_gen_planes_refined 0.007
r_bond_refined_d 0.012
r_scbond_it 3.36
r_angle_refined_deg 1.651
r_mcangle_it 1.825
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4040
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 559

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing