X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 294.0
Details 1.6 M (NH4)2SO4, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.28 α = 90
b = 139.28 β = 90
c = 139.28 γ = 90
Symmetry
Space Group I 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Vertical focusing mirror 2002-06-02
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.97900 SSRL BL9-1

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
2.8 40 99.2 0.039 0.039 -- 4.4 11287 11287 0.0 0.0 94.0
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)
2.8 2.9 99.2 0.418 0.418 2.0 3.1 1104

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 2.8 29.7 0.0 0.0 11219 10682 537 99.75 -- 0.24865 0.24681 0.28527 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 2.8 2.872 -- 39 786 0.393 0.3 -- 99.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.318
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.081
r_mcangle_it 0.607
r_scbond_it 0.525
r_nbd_refined 0.16
r_scangle_it 0.879
r_bond_refined_d 0.007
r_gen_planes_refined 0.003
r_dihedral_angle_2_deg 35.102
r_dihedral_angle_1_deg 6.097
r_nbtor_refined 0.313
r_symmetry_hbond_refined 0.168
r_xyhbond_nbd_refined 0.172
r_dihedral_angle_3_deg 16.997
r_chiral_restr 0.071
r_symmetry_vdw_refined 0.125
r_mcbond_it 0.338
r_dihedral_angle_4_deg 19.664
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2095
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 18

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
Blu-Ice data collection
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
AMoRE phasing