6AOO | pdb_00006aoo

2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HHP	PDB entry 3HHP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	20.0 mg/mL protein in 0.3 M sodium chloride, 0.01 M HEPES, pH 7.5, screen: 0.1 M lithium sulfate, 0.1 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 20% w/v PEG3350, 0.25 mM D-Malic acid, cryoprotectant: paratone

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.688	α = 90
b = 94.119	β = 121.7
c = 73.215	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 9M	Si(111)	2017-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07822	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	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	2.15	30	97.5	0.122	0.122	0.039	18.5	10.9		33055		-3	34.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	99.3		0.749	0.749	0.229	0.876	4.3	11.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 3HHP	2.15	29.68	31307	1660	97.44	0.18516	0.18236	0.19	0.23732	0.25	RANDOM	49.215

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]
5.85		2.49	-3.33		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.656
r_dihedral_angle_4_deg	10.18
r_dihedral_angle_3_deg	8.844
r_long_range_B_refined	6.704
r_long_range_B_other	6.637
r_scangle_other	3.228
r_mcangle_it	2.963
r_mcangle_other	2.963
r_dihedral_angle_1_deg	2.192
r_scbond_it	2.014
r_scbond_other	2.001
r_mcbond_it	1.903
r_mcbond_other	1.9
r_angle_refined_deg	1.429
r_angle_other_deg	0.879
r_chiral_restr	0.078
r_gen_planes_refined	0.023
r_gen_planes_other	0.02
r_bond_refined_d	0.009
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	4662
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing