X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details PEG 4000, sodium acetate, n-butanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.94 α = 90
b = 46.94 β = 90
c = 111.33 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-1 Mirrors 2002-02-21
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97895 APS 19-BM

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
1.25 30 96.7 0.043 -- -- 3.1 66271 64084 -- -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)
1.25 1.29 89.4 0.172 -- 2.8 2.0 5918

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 1.25 30.0 -- 0.0 59607 56323 6344 94.49 0.16294 0.16294 0.16044 0.18501 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 1.25 1.318 8073 828 7311 0.171 0.202 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic temperature factors
Mean Isotropic B 11.333
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.079
r_sphericity_bonded 1.554
r_angle_refined_deg 1.315
r_nbd_other 0.208
r_gen_planes_refined 0.004
r_scbond_it 1.92
r_rigid_bond_restr 0.947
r_dihedral_angle_2_deg 14.593
r_dihedral_angle_1_deg 3.543
r_xyhbond_nbd_refined 0.137
r_gen_planes_other 0.001
r_mcbond_it 0.77
r_scangle_it 3.097
r_sphericity_free 1.973
r_bond_refined_d 0.01
r_nbd_refined 0.241
r_symmetry_hbond_refined 0.214
r_bond_other_d 0.001
r_symmetry_vdw_other 0.22
r_angle_other_deg 0.743
r_mcangle_it 1.344
r_symmetry_vdw_refined 0.132
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2081
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 329

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
HKL-2000 data reduction
SCALEPACK data scaling
CNS phasing