9PVN | pdb_00009pvn

Human malic enzyme 3 complex with inhibitor NPD-389 at 1.82 Angstrom.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		In lab model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane pH: 8.5, 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.624	α = 90
b = 60.275	β = 90.81
c = 159.501	γ = 90

Symmetry
Space Group	I 1 2 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	PIXEL	DECTRIS EIGER X 16M		2023-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.82	45.483	99	0.988	6.1	3.6		114678

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	1.82	1.85			0.428	0.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	1.82	45.483	114636	5892	98.984	0.19	0.1894	0.1976	0.2075	0.2134	27.829

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]
-1.468		0.709	0.212		1.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.901
r_dihedral_angle_3_deg	12.085
r_dihedral_angle_1_deg	5.52
r_dihedral_angle_2_deg	5.452
r_lrange_it	4.572
r_lrange_other	4.384
r_scangle_it	2.765
r_scangle_other	2.765
r_mcangle_it	2.052
r_mcangle_other	2.052
r_scbond_it	1.606
r_scbond_other	1.606
r_mcbond_it	1.22
r_mcbond_other	1.219
r_angle_refined_deg	1.017
r_dihedral_angle_other_2_deg	0.78
r_angle_other_deg	0.378
r_nbd_refined	0.202
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.111
r_symmetry_xyhbond_nbd_refined	0.111
r_nbd_other	0.11
r_symmetry_xyhbond_nbd_other	0.081
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.051
r_chiral_restr_other	0.004
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8666
Nucleic Acid Atoms
Solvent Atoms	861
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing