4NFR | pdb_00004nfr

Human brain aspartoacylase mutant E285A 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, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.736	α = 90
b = 147.736	β = 90
c = 102.738	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	Kirkpatrick-Baez mirrors	2013-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97934	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	3	50	90	0.101	9.4	2.6		17286	2	2	49.8

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	3	3.11	90		0.188	3	1.3	377

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB Entry 2o4h	3	46.76	2	39582	16360	886	73.79	0.19344	0.19089	0.19	0.24052	0.24	RANDOM	72.212

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]
3.64			3.64		-7.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.696
r_dihedral_angle_4_deg	22.948
r_dihedral_angle_3_deg	18.245
r_long_range_B_refined	8.661
r_long_range_B_other	8.627
r_dihedral_angle_1_deg	5.899
r_scangle_other	5.538
r_mcangle_it	5.387
r_mcangle_other	5.381
r_mcbond_it	3.281
r_mcbond_other	3.28
r_scbond_it	3.241
r_scbond_other	3.24
r_angle_refined_deg	1.148
r_angle_other_deg	0.897
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4834
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	28

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4	phasing