X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 290.0
Details 12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.45 α = 90
b = 175.9 β = 96.55
c = 67.56 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 -- 2005-09-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 1.11587 ALS 5.0.3

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
2.29 50 93.8 0.145 -- -- 3.1 51915 51915 0.0 -4.0 --
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)
2.29 2.38 87.0 0.571 -- 1.9 -- --

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 2.3 45.55 -- -- -- 43380 2308 93.83 -- 0.25085 0.24843 0.29537 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 -- 169 2990 0.301 0.391 -- 87.39
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.106
Anisotropic B[1][1] -1.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.51
Anisotropic B[2][2] -2.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.33
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.073
r_dihedral_angle_2_deg 31.323
r_xyhbond_nbd_other 0.053
r_mcangle_it 0.612
r_dihedral_angle_1_deg 6.662
r_xyhbond_nbd_refined 0.171
r_gen_planes_refined 0.003
r_mcbond_it 0.524
r_dihedral_angle_3_deg 14.71
r_symmetry_vdw_other 0.191
r_bond_other_d 0.001
r_angle_refined_deg 1.217
r_symmetry_vdw_refined 0.177
r_symmetry_hbond_refined 0.145
r_nbtor_other 0.079
r_gen_planes_other 0.001
r_bond_refined_d 0.009
r_mcbond_other 0.069
r_angle_other_deg 0.85
r_nbtor_refined 0.18
r_nbd_refined 0.165
r_scangle_it 1.308
r_scbond_it 0.877
r_dihedral_angle_4_deg 13.268
r_nbd_other 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6614
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 470

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
Blu-Ice data collection
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
PHASER phasing