3FW0

Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) bound to alpha-hydroxyhippuric acid (non-peptidic substrate)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPALcc native, being deposited at the same time as this structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M sodium acetate pH=4.8, 0.5mM mercury(II) acetate - 0.2ml mother liquor in reservoir. Then, crystals soaked in 5mM hydroxyhippuric acid for several hours, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5651.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.93α = 90
b = 75.08β = 90
c = 97.026γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMonochromator Kohzu HLD-4 Double Crystal2008-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID1.00724APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.559.3499.60.07523.56.81334713347
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.5998.90.482.75.71306

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPALcc native, being deposited at the same time as this structure2.5259.34133471264865599.090.209390.206720.26019RANDOM44.912
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]
1.120.24-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.247
r_dihedral_angle_4_deg19.785
r_dihedral_angle_3_deg17.925
r_dihedral_angle_1_deg7.552
r_angle_refined_deg1.246
r_scangle_it1.237
r_scbond_it1.213
r_mcangle_it0.541
r_nbtor_refined0.31
r_mcbond_it0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.247
r_dihedral_angle_4_deg19.785
r_dihedral_angle_3_deg17.925
r_dihedral_angle_1_deg7.552
r_angle_refined_deg1.246
r_scangle_it1.237
r_scbond_it1.213
r_mcangle_it0.541
r_nbtor_refined0.31
r_mcbond_it0.31
r_symmetry_hbond_refined0.224
r_nbd_refined0.195
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.126
r_chiral_restr0.115
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2619
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms17

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling