X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details Na/Cacodylate, MgCl2, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.88 α = 90
b = 104.88 β = 90
c = 70.43 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2005-02-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 PHOTON FACTORY AR-NW12A

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 50 99.8 -- 0.089 -- 8.0 -- 34806 -- -- --
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 1.93 99.5 -- 0.45 -- 4.9 --

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 1.9 42.07 -- 0.0 -- 33041 1750 100.0 -- 0.1882 0.18657 0.2191 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 1.949 -- 124 2449 0.307 0.358 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.945
Anisotropic B[1][1] -0.7
Anisotropic B[1][2] -0.35
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.05
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.783
r_scbond_it 2.925
r_mcangle_it 2.08
r_mcbond_it 1.186
r_symmetry_hbond_refined 0.256
r_bond_refined_d 0.017
r_angle_refined_deg 1.706
r_dihedral_angle_1_deg 6.095
r_dihedral_angle_2_deg 33.637
r_dihedral_angle_3_deg 17.916
r_dihedral_angle_4_deg 20.486
r_chiral_restr 0.12
r_gen_planes_refined 0.007
r_nbd_refined 0.225
r_nbtor_refined 0.315
r_xyhbond_nbd_refined 0.225
r_symmetry_vdw_refined 0.228
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2095
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 246

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
MOLREP model building
HKL-2000 data collection