X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 298.0
Details Isopropanol, CaCl2, sodium acetate, pluronic F-68, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.94 α = 90
b = 113.94 β = 90
c = 128.83 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-02-06
CCD ADSC QUANTUM 4 -- 2000-05-16
Diffraction Radiation
Monochromator Protocol
double crystal monochromator MAD
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97935, 0.97906, 0.93222 SSRL BL9-2
SYNCHROTRON SSRL BEAMLINE BL9-2 0.99981 SSRL BL9-2

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
2.8 57 98.0 -- -- -- -- 12228 12228 0.0 0.0 --
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)
2.8 2.9 90.1 -- -- -- -- --

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
MAD 2.8 57.0 -- 2.0 12228 11237 991 95.97 0.25748 0.2574 0.25548 0.28009 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 2.8 2.949 1474 144 1474 0.287 0.364 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.315
Anisotropic B[1][1] 1.79
Anisotropic B[1][2] 0.89
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.68
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.167
r_symmetry_vdw_refined 0.077
r_xyhbond_nbd_refined 0.152
r_nbd_refined 0.141
r_gen_planes_refined 0.009
r_chiral_restr 0.139
r_dihedral_angle_3_deg 22.269
r_dihedral_angle_1_deg 3.898
r_angle_refined_deg 1.927
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1701
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 5

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
shake version: n' bake model building