X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 298.0
Details PEG2KMME 30%, NaCitr. 0.1M, NaAcetate 0.2M, Tacsimate 1%, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.41 α = 90
b = 71.41 β = 90
c = 147.72 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2005-11-27
Diffraction Radiation
Monochromator Protocol
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9798 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
1.7 61.9 98.84 0.096 -- -- 12.4 24053 23774 2.0 2.0 22.3
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)
1.7 1.76 82.4 0.556 -- 1.58 4.2 4627

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 1.7 61.9 -- 0.0 24053 23774 1281 98.84 0.22 0.21265 0.21109 0.24166 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 1.699 1.743 -- 86 1518 0.291 0.315 -- 87.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.219
Anisotropic B[1][1] 0.39
Anisotropic B[1][2] 0.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.58
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.829
r_scbond_it 2.677
r_angle_refined_deg 1.171
r_bond_refined_d 0.01
r_symmetry_vdw_refined 0.224
r_nbtor_refined 0.298
r_scangle_it 4.195
r_mcangle_it 1.362
r_dihedral_angle_3_deg 13.862
r_dihedral_angle_4_deg 14.214
r_symmetry_hbond_refined 0.161
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 4.278
r_nbd_refined 0.216
r_xyhbond_nbd_refined 0.164
r_chiral_restr 0.072
r_dihedral_angle_2_deg 29.147
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.04
Luzzati Sigma A (Observed) 0.038
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.041
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1345
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 195

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
SBC-Collect data collection
HKL-2000 data scaling