3TOZ | pdb_00003toz

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NPD	pdb entry 1NPD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3); Screen: Classics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG R3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.13	α = 90
b = 78.434	β = 90.49
c = 214.829	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 225 mm CCD	Beryllium lenses	2011-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.2	30	98.2	0.096	12.3	3.8	117864	117864		-3	37

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	2.2	2.24	97.3		0.525	2.5	3.9	5755

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 1NPD	2.2	29.63	110577	110577	5836	98.18	0.19855	0.19855	0.19547	0.2	0.25584	0.26	RANDOM	33.413

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]
-3.3		-2.45	4.26		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.159
r_dihedral_angle_4_deg	11.626
r_dihedral_angle_3_deg	9.635
r_scangle_it	4.281
r_scbond_it	2.951
r_dihedral_angle_1_deg	2.274
r_mcangle_it	1.634
r_angle_refined_deg	1.568
r_mcbond_it	0.97
r_angle_other_deg	0.856

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.159
r_dihedral_angle_4_deg	11.626
r_dihedral_angle_3_deg	9.635
r_scangle_it	4.281
r_scbond_it	2.951
r_dihedral_angle_1_deg	2.274
r_mcangle_it	1.634
r_angle_refined_deg	1.568
r_mcbond_it	0.97
r_angle_other_deg	0.856
r_mcbond_other	0.297
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17938
Nucleic Acid Atoms
Solvent Atoms	1010
Heterogen Atoms	396

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.