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
IMAGE PLATE RIGAKU RAXIS IV -- 2003-10-20
CCD MARRESEARCH -- 2003-10-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.54 -- --
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1

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_scangle_it 4.865
r_scbond_it 3.508
r_mcangle_it 2.08
r_mcbond_other 0.319
r_mcbond_it 1.453
r_symmetry_hbond_refined 0.32
r_symmetry_vdw_other 0.322
r_symmetry_vdw_refined 0.254
r_xyhbond_nbd_refined 0.161
r_nbtor_other 0.085
r_nbtor_refined 0.176
r_nbd_other 0.181
r_bond_refined_d 0.019
r_bond_other_d 0.001
r_angle_refined_deg 1.645
r_angle_other_deg 0.895
r_dihedral_angle_1_deg 6.6
r_dihedral_angle_2_deg 33.646
r_dihedral_angle_3_deg 11.179
r_dihedral_angle_4_deg 10.057
r_chiral_restr 0.118
r_gen_planes_refined 0.009
r_gen_planes_other 0.003
r_nbd_refined 0.213
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SHELXS Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement