2WYV | pdb_00002wyv

High resolution structure of Thermus thermophilus enoyl-acyl carrier protein reductase NAD-form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WYU	PDB ENTRY 2WYU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.4		20% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.27	α = 90
b = 107.8	β = 95.89
c = 85.98	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	ADSC CCD	TOROIDAL FOCUSING MIRROR	2008-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.85	40	95.9	0.06	10.1	2.9		77770			21.5

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	1.85	1.95	89.2		0.41	2.2	2.5

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	PDB ENTRY 2WYU	1.86	39.75	76657	1098	95.87	0.18277	0.18199	0.19	0.23926	0.24	RANDOM	22.445

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]
1.75		-2.35	-2.46		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.539
r_dihedral_angle_4_deg	14.824
r_dihedral_angle_3_deg	13.185
r_dihedral_angle_1_deg	5.948
r_scangle_it	3.791
r_scbond_it	2.214
r_angle_refined_deg	1.48
r_mcangle_it	1.48
r_angle_other_deg	1.016
r_mcbond_it	0.817
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.207
r_mcbond_other	0.183
r_nbd_other	0.175
r_symmetry_vdw_other	0.175
r_nbtor_refined	0.167
r_metal_ion_refined	0.154
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.135
r_chiral_restr	0.088
r_nbtor_other	0.081
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7695
Nucleic Acid Atoms
Solvent Atoms	545
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing