X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details NaCl, Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.11 α = 90
b = 50.11 β = 90
c = 153.5 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2002-10-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2 21 96.7 -- 0.035 -- 3.0 29163 28209 0.0 3.0 --
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)
2.0 2.07 74.1 -- 0.137 -- -- --

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 2.0 18.9 0.0 0.0 25674 25674 2355 96.38 0.20625 0.20625 0.20168 0.2559 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 2.0 2.051 -- 114 1382 0.236 0.268 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.796
Anisotropic B[1][1] 0.74
Anisotropic B[1][2] 0.37
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.12
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.09
r_nbd_other 0.25
r_nbd_refined 0.25
r_gen_planes_other 0.014
r_gen_planes_refined 0.011
r_chiral_restr 0.125
r_dihedral_angle_1_deg 6.974
r_angle_other_deg 1.033
r_angle_refined_deg 1.818
r_bond_other_d 0.002
r_bond_refined_d 0.022
r_xyhbond_nbd_refined 0.192
r_symmetry_vdw_refined 0.226
r_symmetry_vdw_other 0.258
r_symmetry_hbond_refined 0.218
r_mcbond_it 1.341
r_mcangle_it 2.41
r_scbond_it 3.089
r_scangle_it 5.053
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3016
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 198

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
MOLREP V. 7.3.01 Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement