X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 277.0
Details 18% (w/v) PEG 6000 and 0.1 M sodium acetate pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.46 α = 90
b = 45.51 β = 90
c = 77.75 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2004-06-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 32-ID 1.000 APS 32-ID

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
1.18 40 96.7 0.072 -- -- -- 54241 52457 -- -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)
1.18 1.22 74.6 0.332 -- -- -- --

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
Rigid Body Refinement 1.18 22.81 -- 0.0 52405 52405 2920 96.71 0.13 0.13 0.129 0.155 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 1.18 1.208 2738 152 2586 0.195 0.215 -- 69.32
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.18
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.51
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.122
r_nbtor_refined 0.18
r_mcangle_it 2.866
r_dihedral_angle_1_deg 7.047
r_scangle_it 5.242
r_symmetry_hbond_refined 0.21
r_symmetry_vdw_refined 0.417
r_sphericity_free 9.638
r_metal_ion_refined 0.362
r_mcbond_it 1.917
r_sphericity_bonded 4.631
r_dihedral_angle_4_deg 10.899
r_nbd_refined 0.333
r_bond_refined_d 0.019
r_gen_planes_other 0.011
r_dihedral_angle_3_deg 10.44
r_scbond_it 3.668
r_angle_other_deg 1.585
r_gen_planes_refined 0.01
r_xyhbond_nbd_refined 0.173
r_nbtor_other 0.088
r_dihedral_angle_2_deg 33.278
r_nbd_other 0.241
r_symmetry_vdw_other 0.288
r_bond_other_d 0.002
r_rigid_bond_restr 1.949
r_mcbond_other 0.952
r_angle_refined_deg 1.795
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1146
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 285

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 1.701