X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Temperature 294.0
Details 1 uL prot + 1 uL reservoir (PEG 6000 30%, 0.1 M tris-HCl) + 2uL NADP 2 mM, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.15 α = 90
b = 70.85 β = 90.3
c = 104.49 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-10-12
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
1.55 20 97.0 -- 0.046 -- 4.09 -- 135727 -- 0.0 --
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)
1.55 1.61 85.5 -- 0.426 3.01 3.46 --

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
SAD 1.55 20.0 -- -- 132172 131035 6895 99.14 -- 0.1903 0.18863 0.22191 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 1.55 1.59 -- 403 8138 0.226 0.27 -- 90.17
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.34
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.665
r_nbtor_refined 0.304
r_scbond_it 2.06
r_symmetry_hbond_refined 0.235
r_dihedral_angle_1_deg 5.275
r_nbd_refined 0.217
r_symmetry_vdw_refined 0.234
r_chiral_restr 0.15
r_dihedral_angle_3_deg 14.118
r_dihedral_angle_4_deg 18.566
r_xyhbond_nbd_refined 0.133
r_scangle_it 3.099
r_gen_planes_refined 0.005
r_mcbond_it 0.819
r_xyhbond_nbd_other 0.14
r_mcangle_it 1.23
r_dihedral_angle_2_deg 36.564
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8498
Nucleic Acid Atoms 0
Heterogen Atoms 208
Solvent Atoms 424

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
ProDC data collection
XDS data scaling
SHARP phasing