2GZ3 | pdb_00002gz3

Structure of Aspartate Semialdehyde Dehydrogenase (ASADH) from Streptococcus pneumoniae complexed with NADP and aspartate-semialdehyde

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GZ1	PDB Entry: 2GZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	50 mM Citrate pH 6.0 200 mM ammonium acetate 20% PEG 8000 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.348	α = 89.98
b = 64.439	β = 81.06
c = 96.739	γ = 82

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	IMAGE PLATE	RIGAKU RAXIS IV		2006-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.3	43.58	92.7	0.113	6.6	3.3		95735	2	2

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	2.3	2.38	89.6		0.293	3.3	3.31	5581

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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: 2GZ1	2.1	30.01	75010	75010	3769	91.68	0.214	0.214	0.211	0.21	0.277	0.27	RANDOM	22.018

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]
0.27		-0.03	-0.04	-0.01	-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.697
r_dihedral_angle_4_deg	17.199
r_dihedral_angle_3_deg	16.158
r_dihedral_angle_1_deg	6.103
r_scangle_it	2.285
r_scbond_it	1.444
r_angle_refined_deg	1.334
r_mcangle_it	0.846
r_mcbond_it	0.511
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.697
r_dihedral_angle_4_deg	17.199
r_dihedral_angle_3_deg	16.158
r_dihedral_angle_1_deg	6.103
r_scangle_it	2.285
r_scbond_it	1.444
r_angle_refined_deg	1.334
r_mcangle_it	0.846
r_mcbond_it	0.511
r_nbtor_refined	0.3
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.162
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10759
Nucleic Acid Atoms
Solvent Atoms	808
Heterogen Atoms	224

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
PHASER	phasing

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.