X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 1,6 hexanediol, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47 α = 90
b = 47 β = 90
c = 120.14 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-03-03
Diffraction Radiation
Monochromator Protocol
super-bend magnet MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 0.9765, 0.9766, 0.9643 ALS 8.2.1

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
1.8 30 99.8 0.073 -- -- 18.0 7887 7658 0.0 0.0 25.5
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)
1.8 1.85 100.0 0.43 -- 2.8 18.0 625

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 1.8 20.0 -- 0.0 7887 7304 538 99.72 0.21176 0.21176 0.20867 0.25724 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 1.8 1.847 -- 40 510 0.223 0.286 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.5
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.272
r_nbd_refined 0.263
r_nbtor_other 0.089
r_bond_refined_d 0.034
r_xyhbond_nbd_refined 0.255
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.203
r_mcangle_it 2.708
r_scbond_it 4.341
r_gen_planes_other 0.002
r_sphericity_bonded 2.783
r_dihedral_angle_1_deg 3.826
r_nbd_other 0.255
r_sphericity_free 4.101
r_symmetry_hbond_refined 0.309
r_chiral_restr 0.084
r_angle_refined_deg 1.663
r_gen_planes_refined 0.006
r_angle_other_deg 0.911
r_mcbond_it 1.536
r_scangle_it 7.49
r_rigid_bond_restr 2.504
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 489
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 62

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing