X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 289.0
Details 0.1M Sodium citrate, 0.2M Ammonium acetate, 30% PEG 4000, 10mM ATP, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.31 α = 90
b = 86.95 β = 90
c = 109.64 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Mirrors 2006-11-27
Diffraction Radiation
Monochromator Protocol
Si(111) channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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
1.9 68.2 99.34 0.112 -- -- 8.7 54496 54136 -- 2.0 25.0
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)
1.9 1.95 97.77 0.731 -- 1.57 8.2 4178

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 1.9 35.6 0.0 0.0 54136 54136 2898 99.34 0.17539 0.17539 0.17259 0.22817 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 1.9 1.949 4085 206 3879 0.235 0.338 -- 97.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.183
Anisotropic B[1][1] -0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.87
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.179
r_scbond_it 3.033
r_symmetry_vdw_refined 0.167
r_symmetry_vdw_other 0.277
r_mcbond_it 1.486
r_dihedral_angle_1_deg 5.94
r_gen_planes_other 0.001
r_nbd_other 0.198
r_xyhbond_nbd_refined 0.176
r_bond_refined_d 0.013
r_dihedral_angle_4_deg 15.977
r_dihedral_angle_2_deg 34.946
r_chiral_restr 0.084
r_symmetry_hbond_refined 0.133
r_dihedral_angle_3_deg 13.921
r_bond_other_d 0.001
r_gen_planes_refined 0.005
r_xyhbond_nbd_other 0.016
r_nbd_refined 0.218
r_mcbond_other 0.544
r_mcangle_it 1.726
r_nbtor_other 0.086
r_angle_refined_deg 1.371
r_angle_other_deg 0.934
r_scangle_it 4.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5265
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 433

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
SBC-Collect data collection
HKL-3000 data reduction
HKL-3000 data scaling
MLPHARE phasing