X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.84 α = 90
b = 90.84 β = 90
c = 52.66 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2005-02-06
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
1.9 64.28 99.9 0.086 -- -- 9.2 17434 17228 2.0 2.0 37.0
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 1.97 99.7 0.662 -- 2.7 7.3 3300

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 64.28 -- 0.0 17434 17228 929 98.82 0.19479 0.19479 0.19303 0.22969 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 1.932 -- 62 1078 0.244 0.295 -- 85.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.935
Anisotropic B[1][1] 0.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.15
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 26.646
r_dihedral_angle_4_deg 14.104
r_symmetry_hbond_refined 0.174
r_angle_refined_deg 1.097
r_nbtor_refined 0.299
r_scbond_it 1.589
r_mcbond_it 0.745
r_scangle_it 2.408
r_mcangle_it 1.209
r_dihedral_angle_1_deg 6.554
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.134
r_gen_planes_refined 0.004
r_symmetry_vdw_refined 0.179
r_dihedral_angle_3_deg 14.414
r_nbd_refined 0.185
r_chiral_restr 0.078
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.026
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.04
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1188
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 160

Software

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