5CEF | pdb_00005cef

Cystal structure of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HSK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG8000, Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.59	α = 90
b = 130.96	β = 92.87
c = 91.94	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD		2014-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

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	2.6	66.05	100	0.088	4.4	7.3		55730

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	2.6	2.68	100		0.415	4.4	7.1

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	3hsk	2.6	66.05	52836	2849	99.96	0.1831	0.1812	0.19	0.2202	0.22	RANDOM	45.009

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]
2.8		1.87	-0.19		-2.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.397
r_dihedral_angle_4_deg	15.962
r_dihedral_angle_3_deg	15.562
r_dihedral_angle_1_deg	6.449
r_mcangle_it	5.348
r_mcbond_it	3.525
r_mcbond_other	3.522
r_angle_refined_deg	1.513
r_angle_other_deg	1.183
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.397
r_dihedral_angle_4_deg	15.962
r_dihedral_angle_3_deg	15.562
r_dihedral_angle_1_deg	6.449
r_mcangle_it	5.348
r_mcbond_it	3.525
r_mcbond_other	3.522
r_angle_refined_deg	1.513
r_angle_other_deg	1.183
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10796
Nucleic Acid Atoms
Solvent Atoms	619
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Aimless	data scaling
iMOSFLM	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.