1NPD | pdb_00001npd

X-RAY STRUCTURE OF SHIKIMATE DEHYDROGENASE COMPLEXED WITH NAD+ FROM E.COLI (YDIB) NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER24

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	294	200mM ammonium acetate, 100mM tri-sodium citrate dihydrate, 25% PEG 6000, pH 5.2, temperature 294K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.185	α = 90
b = 157.185	β = 90
c = 39.782	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	BRANDEIS - B4		2002-11-22	M	MULTIPLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.979, 0.9787, 0.92	NSLS	X12C

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	100	99.8	0.092	31.2	10.93		48734		-3	31.7

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)
	2.3	2.37			0.373	5.31		4088

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	MAD	THROUGHOUT	2.3	19.71	1	1	25464	24734	1260	97	0.217	0.217	0.2109	0.274	0.2733	RANDOM	35

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]
-1.15	4.56		-1.15		2.3

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.7
c_scangle_it	3.55
c_scbond_it	2.5
c_mcangle_it	2.34
c_mcbond_it	1.45
c_angle_deg	1.3
c_improper_angle_d	0.93
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4374
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	88

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing