X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details PEG3350, Li2SO4, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62 α = 90
b = 64.18 β = 90
c = 95.38 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 Rigaku confocal --
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --
SYNCHROTRON APS BEAMLINE 19-ID 0.97937 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
2 28.5 99.4 -- 0.086 -- 18.8 -- 24837 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)
2.0 2.05 99.4 -- 0.492 3.1 4.1 1792

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 2.0 28.5 -- -- -- 24835 1330 99.42 -- 0.17736 0.17445 0.23323 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 2.001 2.053 1753 91 1792 0.195 0.284 -- 99.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.598
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.114
r_nbd_refined 0.212
r_dihedral_angle_2_deg 38.42
r_chiral_restr 0.111
r_bond_refined_d 0.017
r_scangle_it 4.248
r_gen_planes_refined 0.007
r_angle_refined_deg 1.567
r_metal_ion_refined 0.108
r_mcangle_it 1.946
r_dihedral_angle_3_deg 15.188
r_symmetry_vdw_refined 0.19
r_nbtor_refined 0.317
r_mcbond_it 1.151
r_dihedral_angle_4_deg 23.813
r_xyhbond_nbd_refined 0.159
r_scbond_it 2.841
r_symmetry_hbond_refined 0.109
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2801
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 326

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHASER, CCP4 Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
CCP4 model building
PHASER model building
HKL-3000 data collection
REFMAC version: 5.2.0019 refinement