X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.3
Temperature 293.0
Details 1.8 M AMS, 100 mM citric acid, 100 mM boric acid , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.91 α = 90
b = 130.91 β = 90
c = 189.37 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Bent mirror 2002-03-21
Diffraction Radiation
Monochromator Protocol
Triangular monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, Hamburg X13

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
2.1 24.8 99.7 0.13 0.13 -- 8.16 56339 56215 2.0 2.0 24.33
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)
2.1 2.14 99.9 0.547 0.547 3.56 6.8 2104

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 2.1 24.77 0.0 0.0 54834 54834 1141 100.0 0.17805 0.17805 0.1775 0.20455 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 2.101 2.156 -- 72 3962 0.199 0.229 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.624
Anisotropic B[1][1] 1.31
Anisotropic B[1][2] 0.65
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.96
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.352
r_symmetry_vdw_other 0.303
r_scangle_it 2.572
r_bond_other_d 0.014
r_nbtor_other 0.084
r_symmetry_hbond_refined 0.23
r_bond_refined_d 0.012
r_mcbond_it 0.472
r_symmetry_vdw_refined 0.194
r_nbd_refined 0.208
r_gen_planes_other 0.023
r_nbd_other 0.243
r_angle_refined_deg 1.286
r_mcangle_it 0.894
r_chiral_restr 0.077
r_gen_planes_refined 0.011
r_dihedral_angle_1_deg 6.281
r_scbond_it 1.528
r_xyhbond_nbd_refined 0.136
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5959
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 406

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing