X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 293.0
Details NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.49 α = 90
b = 54.31 β = 99.02
c = 61.28 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

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
1.75 25 94.8 -- 0.056 -- 2.3 -- 19385 -- -- --
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)
1.75 1.8 84.0 -- 0.36 1.8 -- --

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 1.75 12.0 -- -- -- 18343 994 94.37 -- 0.22518 0.22355 0.25434 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 1.75 1.795 -- 64 1177 0.268 0.324 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.442
Anisotropic B[1][1] 1.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.47
Anisotropic B[2][2] -0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.76
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.272
r_symmetry_vdw_refined 0.106
r_scbond_it 1.962
r_bond_refined_d 0.01
r_gen_planes_other 0.002
r_nbtor_other 0.082
r_symmetry_vdw_other 0.174
r_gen_planes_refined 0.005
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.082
r_mcbond_it 0.907
r_nbd_other 0.225
r_dihedral_angle_1_deg 6.369
r_nbd_refined 0.198
r_angle_refined_deg 1.267
r_chiral_restr 0.086
r_symmetry_hbond_refined 0.038
r_mcangle_it 1.708
r_angle_other_deg 0.77
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.114
Luzzati ESD (R-Free Set) 0.115
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1271
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 71

Software

Software
Software Name Purpose
DENZO data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)