3GN8

X-ray Crystal Structure of AncGR2 in Complex with Dexamethasone


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details 0.5-0.75M ammonium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.22 α = 90
b = 104.22 β = 90
c = 144.17 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate Double Crystal Monochromator Si-220 2008-04-19
Diffraction Radiation
Monochromator Protocol
Double Crystal Si-220 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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
2.5 50 100.0 -- 0.115 -- 7.3 30813 30813 0.0 0.0 52.2
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)
2.5 2.59 100.0 -- 0.44 5.2 7.3 3879

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 2.5 49.01 0.0 0.0 -- 29216 1550 99.98 -- 0.19888 0.1959 0.25467 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 2.5 2.563 -- 103 2174 0.269 0.353 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.643
Anisotropic B[1][1] 0.38
Anisotropic B[1][2] 0.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.507
r_dihedral_angle_1_deg 5.312
r_angle_refined_deg 1.434
r_xyhbond_nbd_refined 0.16
r_bond_refined_d 0.012
r_rigid_bond_restr 4.17
r_dihedral_angle_2_deg 37.805
r_sphericity_bonded 2.404
r_nbd_refined 0.207
r_chiral_restr 0.101
r_mcangle_it 1.499
r_symmetry_vdw_refined 0.233
r_gen_planes_refined 0.005
r_scbond_it 3.979
r_nbtor_refined 0.314
r_mcbond_it 0.895
r_dihedral_angle_4_deg 17.842
r_dihedral_angle_3_deg 19.753
r_symmetry_hbond_refined 0.157
r_sphericity_free 3.867
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.317
Luzzati Resolution Cutoff (Low) 90.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4213
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 154

Software

Software
Software Name Purpose
SERGUI data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling