4TNU | pdb_00004tnu

Human brain aspartoacylase mutant Y231C complex with intermediate analog (N-phosphonomethyl-L-aspartate)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O4H	PDB entry 2O4H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	14% PEG 3350, 0.05M sodium citrate, 0.3M potassium phosphate (dibasic), 3% ethylene glycol, 0.01M DTT

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.959	α = 90
b = 147.959	β = 90
c = 103.456	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2014-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.283	APS	23-ID-D

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	2.9	50	100	0.142	10.7	4.7		25970

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	2.9	3	99.9		0.74	2.1	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 2O4H	2.9	48.88	24598	1320	99.64	0.19913	0.19724	0.2	0.23473	0.23	RANDOM	70.51

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]
1.59			1.59		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.72
r_dihedral_angle_3_deg	17.501
r_dihedral_angle_4_deg	17.28
r_long_range_B_refined	8.744
r_long_range_B_other	8.743
r_scangle_other	6.207
r_mcangle_it	6.106
r_mcangle_other	6.104
r_dihedral_angle_1_deg	6.074
r_mcbond_it	3.94
r_mcbond_other	3.94
r_scbond_it	3.817
r_scbond_other	3.816
r_angle_refined_deg	1.299
r_angle_other_deg	0.879
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	4830
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement