8XAC | pdb_00008xac

Crystal structure of amidase from Pseudonocardia acaciae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5H6T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG8000, NaCl, CAPS, pH 10.5.

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.28	α = 90
b = 165.28	β = 90
c = 160.612	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS EIGER X 4M		2022-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.04	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	3	44.119	99.8	0.992	11.9	14.4		42219

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.1			0.727

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.02	44.119	42214	1940	99.757	0.204	0.2018	0.2072	0.2587	0.2611	55.92

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]
0.853			0.853		-1.706

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.921
r_dihedral_angle_6_deg	15.044
r_lrange_other	8.723
r_lrange_it	8.722
r_dihedral_angle_1_deg	5.892
r_scangle_it	5.342
r_scangle_other	5.341
r_mcangle_it	5.164
r_mcangle_other	5.164
r_dihedral_angle_2_deg	4.11
r_mcbond_it	3.191
r_mcbond_other	3.191
r_scbond_it	3.18
r_scbond_other	3.18
r_angle_refined_deg	1.194
r_angle_other_deg	0.453
r_symmetry_xyhbond_nbd_refined	0.374
r_symmetry_nbd_other	0.227
r_nbd_other	0.222
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.215
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_other	0.129
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.061
r_chiral_restr	0.057
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13545
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
MOLREP	phasing