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 = 81.59 α = 90
b = 81.59 β = 90
c = 210.08 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 ADSC QUANTUM 4 Rh-coated Si mirror 2000-08-26
Diffraction Radiation
Monochromator Protocol
Bent triangular asymmetric cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.900 CHESS F1

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 25 99.3 -- 0.065 -- 8.4 56085 55698 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)
2.0 2.07 97.8 -- 0.412 1.69 5.9 5362

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 2.0 24.92 -- 0.0 56085 52523 2793 99.32 0.19618 0.19618 0.1943 0.23154 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 2.0 2.052 -- 190 3603 0.257 0.324 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 41.151
Anisotropic B[1][1] 1.51
Anisotropic B[1][2] 0.76
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.27
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 16.629
r_scbond_it 14.006
r_mcangle_it 8.675
r_mcbond_it 6.434
r_symmetry_hbond_refined 0.146
r_symmetry_vdw_other 0.398
r_symmetry_vdw_refined 0.506
r_bond_refined_d 0.018
r_bond_other_d 0.084
r_angle_refined_deg 1.626
r_angle_other_deg 1.211
r_dihedral_angle_1_deg 6.206
r_chiral_restr 0.113
r_gen_planes_refined 0.014
r_gen_planes_other 0.031
r_nbd_refined 0.246
r_nbd_other 0.328
r_nbtor_other 0.099
r_xyhbond_nbd_refined 0.166
Coordinate Error
Parameter Value
Luzzati Sigma A (R-Free Set) 0.142
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4350
Nucleic Acid Atoms 0
Heterogen Atoms 148
Solvent Atoms 235

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 version: 5.1.24 refinement