8HPC | pdb_00008hpc

Crystal structure of C171A Mutant of N-carbamyl-D-amino acid amidohydrolase complexed with N-carbamyl-D-Hydroxyphenylglycine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG3350, BIS-TRIS, Ammonium acetate, calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.165	α = 91.4
b = 79.865	β = 98.48
c = 91.07	γ = 92.78

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	Bruker PHOTON II		2022-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.52	46.59	98	0.14	7.3	3		72971

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.52	2.57			0.433

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.52	46.59	69433	3537	98.04	0.21987	0.2181	0.2	0.25324	0.23	RANDOM	22.847

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]
-11.65	-3.22	-11.71	-3.9	-0.58	15.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.839
r_dihedral_angle_4_deg	18.596
r_dihedral_angle_3_deg	14.813
r_dihedral_angle_1_deg	7.568
r_long_range_B_refined	4.871
r_long_range_B_other	4.856
r_scangle_other	3.111
r_mcangle_it	3.074
r_mcangle_other	3.074
r_scbond_it	2.008
r_scbond_other	2.007
r_mcbond_it	1.979
r_mcbond_other	1.978
r_angle_refined_deg	1.436
r_angle_other_deg	1.155
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19127
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	120

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement