X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details bis-tris propane-HCl, sodium chloride, zinc cloride, ammonium acetate, PEG 400, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.63 α = 90
b = 70.63 β = 90
c = 99.61 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-01-01
Diffraction Radiation
Monochromator Protocol
Bent Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C

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
2.2 100 90.4 -- 0.047 -- 4.4 25748 24823 -2.0 -2.0 --
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)
2.2 2.28 43.0 -- 0.405 -- 2.12 1243

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 2.2 60.86 -- 0.0 22393 22393 2429 90.4 0.2192 0.2192 0.21394 0.26743 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 2.2 2.253 -- 67 626 0.376 0.46 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.044
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] -0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.245
r_angle_refined_deg 4.433
r_nbtor_other 0.118
r_chiral_restr 0.215
r_bond_other_d 0.003
r_scangle_it 7.14
r_symmetry_hbond_refined 0.105
r_mcbond_it 1.883
r_nbd_refined 0.244
r_dihedral_angle_1_deg 9.907
r_xyhbond_nbd_refined 0.241
r_mcangle_it 3.239
r_scbond_it 5.245
r_symmetry_vdw_refined 0.16
r_bond_refined_d 0.045
r_gen_planes_refined 0.021
r_angle_other_deg 1.616
r_nbd_other 0.296
r_gen_planes_other 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1431
Nucleic Acid Atoms 896
Heterogen Atoms 6
Solvent Atoms 100

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.22
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing