9E6M | pdb_00009e6m

Crystal structure of the G200R mutant from the maize chloroplastic photosynthetic NADP(+)-dependent malic enzyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OU5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	2.0 M ammonium sulfate, 0.1 M sodium acetate/acetic acid buffer, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.679	α = 90
b = 124.161	β = 90
c = 189.472	γ = 90

Symmetry
Space Group	P 21 21 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		2024-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97623	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	124.16	99.1	0.19	0.213	0.092	0.993	5.3	5.3		63889			50

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.77	99.8		1.687	1.865	0.78	0.62	1.1	5.5

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 (Observed)	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	2.7	50.01	60592	3227	98.74	0.24182	0.23895	0.2522	0.29617	0.3023	RANDOM	61.416

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]
-6.49			9.77		-3.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.281
r_dihedral_angle_4_deg	21.383
r_dihedral_angle_3_deg	20.407
r_long_range_B_refined	13.761
r_long_range_B_other	13.761
r_scangle_other	10.743
r_mcangle_it	9.279
r_mcangle_other	9.278
r_scbond_it	7.119
r_scbond_other	7.119
r_dihedral_angle_1_deg	6.981
r_mcbond_it	6.33
r_mcbond_other	6.33
r_angle_refined_deg	1.707
r_angle_other_deg	1.253
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17433
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing