X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.1M Tris, 1.8M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.5 α = 90
b = 53.06 β = 94.82
c = 100.88 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2004-11-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3

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
2.3 46.92 100.0 0.102 0.102 -- 5.2 40530 40530 2.0 2.0 22.0
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)
2.3 2.42 100.0 0.295 0.295 2.5 5.1 5875

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 2.3 46.92 -- 0.0 40530 40530 2030 99.99 0.194 0.191 0.191 0.249 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 2.3 2.36 2964 130 2834 0.215 0.317 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.837
Anisotropic B[1][1] 0.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.24
Anisotropic B[2][2] -0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.697
r_dihedral_angle_2_deg 40.874
r_dihedral_angle_4_deg 26.915
r_xyhbond_nbd_refined 0.187
r_mcbond_it 0.915
r_chiral_restr 0.133
r_bond_refined_d 0.018
r_gen_planes_refined 0.007
r_scangle_it 3.85
r_symmetry_vdw_refined 0.222
r_scbond_it 2.423
r_nbtor_refined 0.301
r_mcangle_it 1.516
r_symmetry_hbond_refined 0.257
r_angle_refined_deg 1.805
r_dihedral_angle_3_deg 19.824
r_nbd_refined 0.219
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5255
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 406

Software

Software
Software Name Purpose
SCALA data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MOSFLM data reduction