X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 1.6 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.68 α = 90
b = 34.68 β = 90
c = 258.78 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2002-05-07
Diffraction Radiation
Monochromator Protocol
Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.827 SSRL BL11-1

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
1.5 34 74.0 0.054 0.057 -- 4.1 19111 19111 0.0 0.0 12.2
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)
1.5 1.55 43.4 0.125 0.125 1.0 1.84 2600

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 1.5 34.0 -- 0.0 19111 18110 967 71.03 0.1883 0.18831 0.18559 0.2398 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 1.5 1.62 2367 128 2367 0.241 0.345 -- 48.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 20.0
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.984
r_nbd_other 0.249
r_sphericity_bonded 1.38
r_bond_other_d 0.002
r_angle_other_deg 1.267
r_nbtor_other 0.086
r_mcbond_it 1.216
r_dihedral_angle_1_deg 7.17
r_scbond_it 2.775
r_angle_refined_deg 1.917
r_gen_planes_refined 0.009
r_symmetry_vdw_other 0.26
r_bond_refined_d 0.02
r_nbd_refined 0.188
r_gen_planes_other 0.001
r_xyhbond_nbd_refined 0.175
r_symmetry_vdw_refined 0.147
r_symmetry_hbond_refined 0.149
r_scangle_it 4.068
r_chiral_restr 0.116
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.119
Luzzati Sigma A (Observed) 0.076
Luzzati ESD (R-Free Set) 0.123
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1412
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 169

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.22
Blu-Ice data collection
d*TREK data scaling
MOLREP phasing version: V. 7.3