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 PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.63 α = 90
b = 81.63 β = 90
c = 225.68 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 MARRESEARCH -- 2002-08-02
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.255 APS 17-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
3.3 35 95.6 -- 0.079 -- 9.7 13745 13146 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)
3.3 3.33 95.8 -- 0.22 8.6 9.4 316

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 3.31 20.0 -- 0.0 12961 12327 642 95.11 0.236 0.236 0.234 0.259 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 3.31 3.389 -- 51 848 0.204 0.272 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 31.768
Anisotropic B[1][1] -0.55
Anisotropic B[1][2] -0.27
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.82
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 21.592
r_xyhbond_nbd_other 0.32
r_symmetry_vdw_refined 0.262
r_chiral_restr 0.135
r_scangle_it 14.94
r_dihedral_angle_1_deg 7.094
r_nbd_refined 0.372
r_nbd_other 0.354
r_bond_refined_d 0.028
r_bond_other_d 0.001
r_gen_planes_other 0.008
r_nbtor_other 0.058
r_mcangle_it 7.536
r_symmetry_vdw_other 0.325
r_symmetry_hbond_refined 0.228
r_angle_other_deg 1.053
r_gen_planes_refined 0.012
r_scbond_it 10.808
r_xyhbond_nbd_refined 0.226
r_angle_refined_deg 2.619
r_mcbond_it 4.91
Coordinate Error
Parameter Value
Luzzati Sigma A (R-Free Set) 0.539
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4555
Nucleic Acid Atoms 0
Heterogen Atoms 130
Solvent Atoms 0

Software

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