2W25

Crystal structure of Glu104Ala mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6295pH 6.0, reservoir: 100 mM 4-morpholineethanesulfonic acid (Mes), pH 6.0, 0.75 M lithium acetate (LiAc)
Crystal Properties
Matthews coefficientSolvent content
3.968.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.65α = 90
b = 100.65β = 90
c = 99.306γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287IMAGE PLATEMARRESEARCHMIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.152091.30.112.95.6255382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.3294.70.82.25.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IVM2.1571.2524011136794.80.2170.2170.218RANDOM42.6
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.170.17-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.696
r_dihedral_angle_3_deg22.472
r_dihedral_angle_4_deg21.546
r_dihedral_angle_1_deg7.891
r_scangle_it6.61
r_scbond_it3.824
r_angle_refined_deg2.269
r_mcangle_it2.234
r_mcbond_it1.181
r_symmetry_vdw_refined0.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.696
r_dihedral_angle_3_deg22.472
r_dihedral_angle_4_deg21.546
r_dihedral_angle_1_deg7.891
r_scangle_it6.61
r_scbond_it3.824
r_angle_refined_deg2.269
r_mcangle_it2.234
r_mcbond_it1.181
r_symmetry_vdw_refined0.382
r_nbtor_refined0.312
r_symmetry_hbond_refined0.278
r_nbd_refined0.243
r_chiral_restr0.242
r_xyhbond_nbd_refined0.186
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2231
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
REFMACphasing