7PDI | pdb_00007pdi

Crystal structure of the holo-acyl carrier protein (holo-AcpP) from Pseudomonas putida KT2440. Produced as an apo/holo mixture.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 0.1 M Tris Bicine buffer, pH 8.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.492	α = 90
b = 56.973	β = 90
c = 61.937	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2019-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9786	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.69	30.988	100	0.0705	0.9994	14.05	12.3		9120

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.72	100		0.397		9.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1T8K	1.69	30.988	9120	874	99.989	0.208	0.2047	0.22	0.2448	0.25	44.778

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]
0.027			0.061		-0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.664
r_dihedral_angle_4_deg	16.979
r_dihedral_angle_3_deg	14.762
r_lrange_other	10.974
r_lrange_it	10.966
r_scangle_it	9.327
r_scangle_other	9.317
r_scbond_it	6.224
r_scbond_other	6.216
r_dihedral_angle_1_deg	6.029
r_mcangle_it	5.031
r_mcangle_other	5.029
r_mcbond_it	3.525
r_mcbond_other	3.513
r_angle_refined_deg	1.555
r_angle_other_deg	1.341
r_symmetry_xyhbond_nbd_refined	0.281
r_xyhbond_nbd_refined	0.229
r_nbd_other	0.217
r_nbd_refined	0.202
r_symmetry_nbd_other	0.183
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.154
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	651
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing