X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details Before crystallization the protein was concentrated to 10 mg/ml and dialysed into 20 mM Tris, 50 mM NaCl, pH 7.0. The protein was crystallized in sitting drops by mixing 1 ul of protein solution at 10 mg/ml with 1 ul of reservoir solution of 2.2 M (NH4)2SO4, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.41 α = 90
b = 91.41 β = 90
c = 110.88 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-10-14
IMAGE PLATE RIGAKU RAXIS IV -- 2003-10-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
ROTATING ANODE RIGAKU RU300 1.54 -- --

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 14.78 99.93 -- 0.059 -- 6.9 22700 22700 0.0 0.0 --
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 1.795 99.9 -- 0.441 3.7 5.1 --

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
SAD 1.75 14.78 -- 0.0 22700 22700 1239 99.93 0.20735 0.20735 0.20641 0.22479 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 -- 87 1642 0.279 0.295 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.593
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 33.646
r_dihedral_angle_3_deg 11.179
r_bond_refined_d 0.019
r_angle_other_deg 0.895
r_gen_planes_refined 0.009
r_bond_other_d 0.001
r_symmetry_vdw_other 0.322
r_scangle_it 4.865
r_dihedral_angle_1_deg 6.6
r_nbtor_other 0.085
r_mcbond_it 1.453
r_nbd_refined 0.213
r_nbtor_refined 0.176
r_mcangle_it 2.08
r_dihedral_angle_4_deg 10.057
r_xyhbond_nbd_refined 0.161
r_mcbond_other 0.319
r_angle_refined_deg 1.645
r_symmetry_hbond_refined 0.32
r_symmetry_vdw_refined 0.254
r_nbd_other 0.181
r_chiral_restr 0.118
r_gen_planes_other 0.003
r_scbond_it 3.508
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 976
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 177

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
XDS data reduction
XDS data scaling
SHELXS phasing