X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 20.0% polyethylene glycol 6000, 1.0M lithium chloride, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 155.79 α = 90
b = 47.07 β = 90
c = 63.24 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-05-14
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97960,0.97905 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
2.07 27.95 98.7 0.047 -- -- -- -- 29174 -- -3.0 30.352
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)
2.07 2.14 98.7 0.433 -- 2.2 -- --

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
MAD 2.07 27.951 -- 0.0 -- 29123 1479 99.43 -- 0.193 0.191 0.223 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 2.068 2.122 -- 104 2020 0.239 0.252 -- 99.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.66
Anisotropic B[1][1] -1.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.26
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 3.561
r_gen_planes_other 0.002
r_symmetry_hbond_refined 0.035
r_angle_refined_deg 1.525
r_dihedral_angle_4_deg 16.73
r_nbd_other 0.143
r_mcbond_it 1.138
r_nbd_refined 0.175
r_bond_other_d 0.003
r_mcbond_other 0.163
r_dihedral_angle_2_deg 31.513
r_angle_other_deg 1.383
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.095
r_nbtor_refined 0.148
r_symmetry_vdw_refined 0.066
r_mcangle_it 1.689
r_chiral_restr 0.093
r_nbtor_other 0.073
r_scangle_it 4.291
r_scbond_it 3.29
r_symmetry_vdw_other 0.149
r_dihedral_angle_3_deg 11.265
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3445
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 249

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.004
XDS data reduction
SHELXD phasing
autoSHARP phasing