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_scangle_it 2.572
r_scbond_it 1.528
r_mcangle_it 0.894
r_mcbond_it 0.472
r_symmetry_hbond_refined 0.23
r_symmetry_vdw_other 0.303
r_symmetry_vdw_refined 0.194
r_bond_refined_d 0.012
r_bond_other_d 0.014
r_angle_refined_deg 1.286
r_angle_other_deg 1.352
r_dihedral_angle_1_deg 6.281
r_chiral_restr 0.077
r_gen_planes_refined 0.011
r_gen_planes_other 0.023
r_nbd_refined 0.208
r_nbd_other 0.243
r_nbtor_other 0.084
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement