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_scbond_it 1.962
r_mcangle_it 1.708
r_nbd_refined 0.198
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.086
r_dihedral_angle_1_deg 6.369
r_angle_other_deg 0.77
r_angle_refined_deg 1.267
r_bond_other_d 0.002
r_bond_refined_d 0.01
r_nbd_other 0.225
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.082
r_symmetry_vdw_refined 0.106
r_symmetry_vdw_other 0.174
r_symmetry_hbond_refined 0.038
r_mcbond_it 0.907
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMoRE model building
SCALA data reduction
DENZO data collection