9Y3A | pdb_00009y3a

Human malic enzyme 1 complex with NADP+ at 1.9 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	0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate, 0.1 M Tris (base); 0.1 M BICINE, 25% v/v MPD; 25% PEG1000; 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.126	α = 90
b = 181.214	β = 104.838
c = 108.594	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	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	1.91	47.901	100	0.999	10.2	14.2		202104

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	1.91	1.94			0.379	0.7

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	1.91	47.901	202040	10290	99.983	0.198	0.1965	0.2012	0.228	0.2306	49.758

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]
2.682		2.827	-2.047		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.575
r_dihedral_angle_3_deg	12.066
r_dihedral_angle_1_deg	5.465
r_lrange_it	5.419
r_lrange_other	5.371
r_dihedral_angle_2_deg	4.481
r_scangle_it	3.809
r_scangle_other	3.809
r_mcangle_it	2.956
r_mcangle_other	2.956
r_scbond_it	2.284
r_scbond_other	2.284
r_mcbond_it	1.912
r_mcbond_other	1.912
r_angle_refined_deg	0.96
r_angle_other_deg	0.356
r_dihedral_angle_other_2_deg	0.281
r_symmetry_xyhbond_nbd_refined	0.221
r_symmetry_nbd_refined	0.198
r_nbd_refined	0.195
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.172
r_nbd_other	0.134
r_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.073
r_metal_ion_refined	0.07
r_chiral_restr	0.048
r_symmetry_xyhbond_nbd_other	0.033
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	17516
Nucleic Acid Atoms
Solvent Atoms	1150
Heterogen Atoms	224

Software

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