9MYF | pdb_00009myf

Human malic enzyme 2 complex with inhibitor NPD-389

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	0.1 M SPG (Succinic acid, Sodium phosphate monobasic monohydrate, Glycine), 25% PEG-1500, pH= 6.0.

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.048	α = 90
b = 58.923	β = 101.938
c = 106.929	γ = 90

Symmetry
Space Group	C 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		2023-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95372	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	2.45	49.219	100	0.998	9	12		46166			51.4

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	2.45	2.54	100		0.595	0.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.45	49.219	46162	2378	99.95	0.232	0.2294	0.2368	0.278	0.2827	Random selection	66.906

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]
-7.235		-1.707	7.747		0.192

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.082
r_dihedral_angle_6_deg	11.912
r_lrange_it	6.136
r_lrange_other	6.136
r_dihedral_angle_1_deg	5.649
r_dihedral_angle_2_deg	4.022
r_scangle_it	3.958
r_scangle_other	3.958
r_mcangle_it	3.794
r_mcangle_other	3.794
r_scbond_it	2.277
r_scbond_other	2.276
r_mcbond_it	2.265
r_mcbond_other	2.263
r_angle_refined_deg	0.896
r_dihedral_angle_other_2_deg	0.837
r_angle_other_deg	0.322
r_nbd_refined	0.196
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.136
r_nbd_other	0.108
r_symmetry_nbd_refined	0.083
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_refined	0.05
r_chiral_restr	0.041
r_symmetry_xyhbond_nbd_other	0.004
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_chiral_restr_other	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8679
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	243

Software

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