X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 15% PEG 3350, 8% PEG 400, 0.05M LiSO4, 0.1M Na-Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.67 α = 90
b = 120.62 β = 90.87
c = 77.38 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2006-12-19
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
1.79 50 98.0 0.117 -- -- 4.7 88013 83551 -- -- --
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)
1.79 1.83 82.9 0.555 -- 1.73 4.0 --

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 1.79 40.69 -- -- 83551 83551 4413 97.58 -- 0.19875 0.19653 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 1.79 1.84 -- 274 5063 0.261 0.325 -- 79.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.615
Anisotropic B[1][1] -1.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.25
Anisotropic B[2][2] 3.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 36.55
r_symmetry_vdw_other 0.211
r_scbond_it 2.367
r_scangle_it 3.189
r_nbd_refined 0.222
r_dihedral_angle_1_deg 8.15
r_nbd_other 0.194
r_gen_planes_refined 0.006
r_bond_other_d 0.001
r_nbtor_other 0.088
r_mcbond_other 0.237
r_symmetry_vdw_refined 0.126
r_dihedral_angle_3_deg 15.673
r_mcangle_it 1.549
r_angle_other_deg 0.968
r_mcbond_it 1.222
r_angle_refined_deg 1.587
r_symmetry_hbond_refined 0.198
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 14.886
r_nbtor_refined 0.183
r_xyhbond_nbd_refined 0.177
r_chiral_restr 0.101
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6904
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 555

Software

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