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_nbtor_other 0.118
r_nbd_other 0.296
r_nbd_refined 0.244
r_gen_planes_other 0.013
r_gen_planes_refined 0.021
r_chiral_restr 0.215
r_dihedral_angle_1_deg 9.907
r_angle_other_deg 1.616
r_angle_refined_deg 4.433
r_bond_other_d 0.003
r_bond_refined_d 0.045
r_xyhbond_nbd_refined 0.241
r_symmetry_vdw_refined 0.16
r_symmetry_vdw_other 0.245
r_symmetry_hbond_refined 0.105
r_mcbond_it 1.883
r_mcangle_it 3.239
r_scbond_it 5.245
r_scangle_it 7.14
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.22 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.22 refinement