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_scangle_it 14.94
r_scbond_it 10.808
r_mcangle_it 7.536
r_mcbond_it 4.91
r_symmetry_hbond_refined 0.228
r_symmetry_vdw_other 0.325
r_symmetry_vdw_refined 0.262
r_xyhbond_nbd_other 0.32
r_xyhbond_nbd_refined 0.226
r_bond_refined_d 0.028
r_bond_other_d 0.001
r_angle_refined_deg 2.619
r_angle_other_deg 1.053
r_dihedral_angle_1_deg 7.094
r_dihedral_angle_3_deg 21.592
r_chiral_restr 0.135
r_gen_planes_refined 0.012
r_gen_planes_other 0.008
r_nbd_refined 0.372
r_nbd_other 0.354
r_nbtor_other 0.058
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection