X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.96
Temperature 277.0
Details 30.00% polyethylene glycol 4000, 0.20M ammonium acetate, 0.1M sodium acetate pH 4.96, Additive: 0.001 M spermine, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.89 α = 90
b = 102.48 β = 90
c = 154.1 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-11-05
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2

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
1.86 48.62 99.8 0.099 -- -- -- -- 68584 -- -3.0 25.708
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)
1.86 1.93 100.0 1.041 -- 1.65 -- --

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 1.86 48.622 -- 0.0 -- 68515 3468 99.83 -- 0.1913 0.1897 0.2202 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 1.86 1.908 -- 250 4758 0.275 0.333 -- 99.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.6134
Anisotropic B[1][1] 1.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.12
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 5.451
r_scbond_it 4.252
r_gen_planes_refined 0.005
r_bond_refined_d 0.014
r_angle_other_deg 0.894
r_dihedral_angle_2_deg 39.585
r_dihedral_angle_3_deg 13.592
r_mcbond_other 0.633
r_chiral_restr 0.081
r_dihedral_angle_4_deg 14.737
r_angle_refined_deg 1.307
r_mcangle_it 2.493
r_scangle_it 6.157
r_mcbond_it 1.552
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5584
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 560

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
BP3 phasing
XSCALE data scaling
REFMAC refinement version: 5.5.0110
XDS data reduction
SHELXD phasing
autoSHARP phasing