X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 294.0
Details 30% Jeffamine D2001, 0.1M bis Tris, pH 6.0, VAPOR DIFFUSION, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.88 α = 90
b = 120.88 β = 90
c = 192.35 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors 2005-07-04
Diffraction Radiation
Monochromator Protocol
OSMIC MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 1.5418 -- --

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
2.38 20 98.7 -- 0.07 -- 13.7 34099 33656 1.0 1.0 --

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 2.38 20.0 -- 0.0 31886 31886 1705 99.05 0.26627 0.26627 0.26216 0.34506 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 2.38 2.507 -- 263 4430 0.324 0.435 -- 97.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.686
Anisotropic B[1][1] 0.91
Anisotropic B[1][2] 0.45
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.36
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.374
r_angle_refined_deg 1.525
r_scbond_it 1.435
r_dihedral_angle_4_deg 16.46
r_mcbond_other 0.126
r_symmetry_vdw_refined 0.195
r_angle_other_deg 0.893
r_gen_planes_refined 0.005
r_xyhbond_nbd_other 0.116
r_mcbond_it 0.893
r_nbtor_other 0.088
r_nbtor_refined 0.191
r_chiral_restr 0.09
r_symmetry_vdw_other 0.195
r_metal_ion_refined 0.272
r_gen_planes_other 0.003
r_nbd_refined 0.22
r_dihedral_angle_2_deg 35.778
r_scangle_it 2.151
r_bond_other_d 0.004
r_bond_refined_d 0.016
r_dihedral_angle_1_deg 6.797
r_xyhbond_nbd_refined 0.19
r_mcangle_it 1.048
r_dihedral_angle_3_deg 19.287
r_nbd_other 0.183
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5305
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 223

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling
SHARP phasing