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_nbd_refined 0.239
r_gen_planes_refined 0.007
r_chiral_restr 0.102
r_dihedral_angle_2_deg 17.811
r_dihedral_angle_1_deg 4.137
r_angle_refined_deg 1.651
r_bond_refined_d 0.012
r_xyhbond_nbd_refined 0.137
r_symmetry_vdw_refined 0.263
r_symmetry_hbond_refined 0.211
r_mcbond_it 1.366
r_mcangle_it 1.825
r_scbond_it 3.36
r_scangle_it 4.566
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement