X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 5% wt/v PEG 6000, 100 mM TrisCl, pH 8.0, and 1 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.48 α = 90
b = 78.48 β = 90
c = 97.67 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-04-30
Diffraction Radiation
Monochromator Protocol
Double-crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 0.9791, 0.9611 ALS 5.0.2

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
1.91 19.84 98.8 0.083 0.083 -- -- 13441 13441 -- 0.0 19.0
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)
1.914 2.01 94.3 0.322 0.322 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
MAD 1.914 19.84 -- 0.0 13441 13441 664 95.32 0.18325 0.18325 0.18124 0.22275 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 1.914 1.964 -- 24 294 0.236 0.374 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.39
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.346
r_chiral_restr 0.138
r_scangle_it 7.727
r_mcangle_it 2.999
r_nbd_other 0.211
r_scbond_it 4.81
r_bond_other_d 0.001
r_angle_refined_deg 2.155
r_gen_planes_refined 0.01
r_xyhbond_nbd_other 0.088
r_bond_refined_d 0.025
r_symmetry_vdw_other 0.26
r_dihedral_angle_1_deg 5.851
r_gen_planes_other 0.003
r_symmetry_hbond_refined 0.334
r_mcbond_it 1.725
r_nbd_refined 0.263
r_angle_other_deg 0.983
r_symmetry_hbond_other 0.011
r_dihedral_angle_3_deg 16.586
r_xyhbond_nbd_refined 0.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 968
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 122

Software

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