9ZZ5 | pdb_00009zz5

Human malic enzyme 3 complex with NADP+ at 1.88 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	7.5	291	0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH: 7.5, 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.232	α = 90
b = 118.136	β = 90
c = 152.087	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 16M		2024-08-09	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	1.88	49.01	100	0.995	7.6	17.7		112376

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	1.88	1.91			0.528	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	THROUGHOUT	1.88	49.038	112317	5717	99.926	0.188	0.1862	0.1932	0.2141	0.2187	RANDOM	34.993

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]
-0.542			-0.848		1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.204
r_dihedral_angle_3_deg	11.667
r_lrange_it	5.518
r_lrange_other	5.365
r_dihedral_angle_1_deg	5.351
r_dihedral_angle_2_deg	4.445
r_scangle_it	3.313
r_scangle_other	3.313
r_mcangle_it	2.686
r_mcangle_other	2.686
r_scbond_it	1.936
r_scbond_other	1.931
r_dihedral_angle_other_2_deg	1.684
r_mcbond_it	1.602
r_mcbond_other	1.601
r_angle_refined_deg	0.977
r_angle_other_deg	0.369
r_nbd_refined	0.2
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.174
r_nbd_other	0.139
r_xyhbond_nbd_refined	0.128
r_symmetry_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.101
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.05
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	8737
Nucleic Acid Atoms
Solvent Atoms	804
Heterogen Atoms	142

Software

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