2AG5

Crystal Structure of Human DHRS6


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details Ammonium sulphate, Mes, PEG monomethylether 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.09 α = 106.05
b = 62.06 β = 105.95
c = 74.04 γ = 100.97
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 2005-07-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT -- -- --

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
1.84 66.67 89.7 -- -- -- -- 84879 76176 -- -- --
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)
1.84 1.9 52.5 -- -- -- -- --

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 1.84 66.67 -- -- -- 74714 1464 89.75 0.16797 0.16797 0.16691 0.22417 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 1.84 1.888 -- 46 3250 0.204 0.239 -- 52.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.061
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] -0.09
Anisotropic B[1][3] 0.27
Anisotropic B[2][2] -0.36
Anisotropic B[2][3] 0.32
Anisotropic B[3][3] 0.27
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 13.25
r_nbd_refined 0.213
r_mcbond_it 1.018
r_bond_refined_d 0.022
r_nbtor_other 0.088
r_chiral_restr 0.106
r_gen_planes_other 0.001
r_mcbond_other 0.326
r_scangle_it 3.505
r_dihedral_angle_1_deg 6.242
r_xyhbond_nbd_refined 0.178
r_angle_other_deg 0.925
r_symmetry_vdw_other 0.29
r_symmetry_hbond_refined 0.187
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.159
r_angle_refined_deg 1.744
r_dihedral_angle_2_deg 37.364
r_nbd_other 0.193
r_mcangle_it 1.422
r_scbond_it 2.504
r_dihedral_angle_4_deg 17.168
r_nbtor_refined 0.175
r_gen_planes_refined 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7365
Nucleic Acid Atoms 0
Heterogen Atoms 196
Solvent Atoms 868

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
PHASER phasing