X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.6
Temperature 293.0
Details PEG3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHELYENE, tris-(2-carboxyethyl)phosphine hydrochloride , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.61 α = 90
b = 81.61 β = 90
c = 226.65 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 Rosenbaum-Rock vertical focusing mirror 2002-03-05
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal sagittal focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9790 APS 19-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
2.7 30 95.4 -- 0.085 -- 6.6 -- 44260 0.0 -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)
2.7 2.8 84.6 -- 0.536 -- 2.7 3915

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
SAD/DM 2.7 20.0 -- 0.0 22832 22706 1216 96.45 0.246 0.246 0.244 0.288 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 2.7 2.769 -- 90 1467 0.322 0.399 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 39.163
Anisotropic B[1][1] 0.56
Anisotropic B[1][2] 0.28
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.84
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_xyhbond_nbd_refined 0.204
r_symmetry_vdw_other 0.41
r_gen_planes_other 0.003
r_chiral_restr 0.1
r_nbd_other 0.349
r_symmetry_hbond_refined 0.565
r_dihedral_angle_1_deg 5.664
r_symmetry_hbond_other 0.592
r_angle_other_deg 0.77
r_mcangle_it 13.703
r_scbond_it 20.052
r_scangle_it 25.098
r_dihedral_angle_3_deg 22.895
r_nbd_refined 0.374
r_xyhbond_nbd_other 0.115
r_symmetry_vdw_refined 0.365
r_gen_planes_refined 0.006
r_mcbond_it 11.309
r_bond_other_d 0.0
r_angle_refined_deg 1.818
Coordinate Error
Parameter Value
Luzzati Sigma A (R-Free Set) 0.36
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4294
Nucleic Acid Atoms 0
Heterogen Atoms 127
Solvent Atoms 69

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SnB phasing
CNS refinement
SHARP phasing
REFMAC refinement version: 5.1.24
CNS phasing