X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.01 α = 90
b = 46.35 β = 90
c = 57.09 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
CCD MAR CCD 165 mm MIRRORS 2002-03-07
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6

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
1.06 15.99 99.0 0.052 -- -- 2.8 35252 34899 -- 2.0 10.57
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)
1.06 1.08 99.1 0.325 -- 2.1 2.7 1716

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 1.06 15.99 -- -- 33683 33127 1747 98.35 -- 0.13796 0.13706 0.15547 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 1.06 1.09 2173 128 2173 0.289 0.319 -- 89.39
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 16.745
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 3.114
r_nbtor_refined 0.361
r_angle_refined_deg 2.728
r_scangle_it 8.072
r_sphericity_bonded 9.123
r_symmetry_vdw_refined 0.185
r_mcangle_it 4.096
r_sphericity_free 17.137
r_rigid_bond_restr 3.455
r_bond_refined_d 0.028
r_symmetry_hbond_refined 0.32
r_dihedral_angle_2_deg 28.324
r_metal_ion_refined 0.053
r_dihedral_angle_1_deg 6.827
r_chiral_restr 0.171
r_scbond_it 5.747
r_dihedral_angle_3_deg 12.413
r_gen_planes_refined 0.013
r_xyhbond_nbd_refined 0.385
r_nbd_refined 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 738
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 191

Software

Software
Software Name Purpose
Marccd data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling