X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details 25 MM NA ACETATE, 25 MM NA CITRATE PH 5.6, 7% PEG 4000, 30% GLYCEROL

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.24 α = 90
b = 145.34 β = 90
c = 159.46 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH PREMIRROR, TRIANGULAR MONOCHROMATOR, BENT MIRROR --
Diffraction Radiation
Monochromator Protocol
MIRROR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, Hamburg BW7B

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
1.89 20 99.6 0.048 -- -- 5.34 -- 134420 -- -- --
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)
1.89 2.0 99.9 0.3566 -- 4.32 4.15 --

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
SIRAS 1.89 20.0 -- -- -- 125806 6720 99.2 -- 0.171 0.17 0.191 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 1.9 1.94 -- 712 8206 0.23 0.235 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.25
Anisotropic B[1][1] -1.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.6
RMS Deviations
Key Refinement Restraint Deviation
r_metal_ion_refined 0.143
r_symmetry_vdw_refined 0.182
r_scangle_it 6.073
r_symmetry_vdw_other 0.261
r_mcangle_it 3.187
r_mcbond_it 1.926
r_bond_refined_d 0.02
r_nbd_refined 0.222
r_nbtor_other 0.087
r_xyhbond_nbd_refined 0.135
r_dihedral_angle_1_deg 6.654
r_nbd_other 0.26
r_gen_planes_other 0.014
r_angle_other_deg 0.903
r_gen_planes_refined 0.012
r_chiral_restr 0.113
r_bond_other_d 0.002
r_angle_refined_deg 1.7
r_symmetry_hbond_refined 0.208
r_scbond_it 4.032
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7637
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 760

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHELXD phasing
DM phasing
REFMAC refinement version: 5.1.19