X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 1.6M tri-Na citrate dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.35 α = 90
b = 23.24 β = 92.47
c = 44.72 γ = 90
Symmetry
Space Group P 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 mirrors 2009-05-07
Diffraction Radiation
Monochromator Protocol
Si-111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.97780 BESSY 14.1

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
1.4 40.5 27.0 0.063 0.063 -- -- -- 11077 5.4 5.3 --
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)
1.4 -- 39.0 0.505 0.505 -- -- 742

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 1.4 23.24 -- -- -- 9922 523 100.0 0.20328 0.20328 0.20222 0.22243 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 1.4 1.436 -- 38 719 0.232 0.23 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.0
Anisotropic B[1][1] 0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.22
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.206
r_mcbond_other 0.316
r_scangle_it 3.357
r_dihedral_angle_1_deg 6.186
r_dihedral_angle_4_deg 21.157
r_nbd_refined 0.239
r_angle_refined_deg 1.495
r_xyhbond_nbd_refined 0.244
r_symmetry_vdw_refined 0.252
r_mcbond_it 1.215
r_bond_other_d 0.014
r_dihedral_angle_2_deg 29.841
r_dihedral_angle_3_deg 10.715
r_mcangle_it 1.623
r_gen_planes_refined 0.007
r_gen_planes_other 0.002
r_bond_refined_d 0.016
r_chiral_restr 0.111
r_angle_other_deg 1.009
r_symmetry_vdw_other 0.311
r_scbond_it 2.544
r_nbtor_refined 0.183
r_symmetry_hbond_refined 0.393
r_nbtor_other 0.087
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.071
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 446
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 36

Software

Software
Software Name Purpose
RAYONICS data collection version: MX-225
MOLREP phasing
REFMAC refinement version: 5.2.0019
XDS data reduction
XSCALE data scaling