X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 2.5M ammonium sulphate, 0.1M Hepes, saturating tetrahydroNAD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.27 α = 90
b = 118.89 β = 90
c = 180.71 γ = 90
Symmetry
Space Group I 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2004-02-01
Diffraction Radiation
Monochromator Protocol
diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 1 ESRF ID14-1

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
1.3 20 89.2 0.097 -- -- 4.2 123781 123781 0.0 0.0 18.0
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)
1.3 1.34 85.4 0.493 -- 2.3 3.4 --

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 1.4 12.0 0.0 0.0 94812 94812 4985 89.2 0.1557 0.15696 0.1557 0.18063 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 1.4 1.436 -- 357 6881 0.269 0.279 -- 85.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.72
Anisotropic B[1][1] -2.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.1
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 35.676
r_xyhbond_nbd_refined 0.156
r_scbond_it 3.437
r_angle_refined_deg 1.837
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.177
r_dihedral_angle_1_deg 6.242
r_dihedral_angle_3_deg 12.489
r_chiral_restr 0.107
r_gen_planes_other 0.001
r_nbtor_refined 0.182
r_mcangle_it 2.267
r_nbd_other 0.21
r_bond_refined_d 0.017
r_sphericity_bonded 8.683
r_mcbond_it 1.833
r_symmetry_hbond_refined 0.152
r_scangle_it 4.558
r_sphericity_free 9.738
r_nbd_refined 0.212
r_dihedral_angle_4_deg 17.92
r_nbtor_other 0.084
r_gen_planes_refined 0.01
r_mcbond_other 1.193
r_angle_other_deg 0.975
r_symmetry_vdw_other 0.219
r_rigid_bond_restr 1.875
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2807
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 684

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
ADSC data collection version: Quantum
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing