6BAL | pdb_00006bal

2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae in Complex with L-Malate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	Protein: 20.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M Ammonium formate, 20% (w/v) PEG3350, 0.25mM DL-Malic acid; Cryo: paratone.

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.108	α = 71.09
b = 78.079	β = 75.44
c = 114.029	γ = 68.06

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD	C(111)	2017-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.1	30	98.2	0.093	0.093	0.108	0.054	13.4	4		126522		-3	28.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	97.2		0.662	0.662	0.77	0.392	0.665	2.1	3.9

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	3HHP	2.1	29.75	120245	6277	97.85	0.17202	0.16958	0.18	0.21869	0.22	RANDOM	35.765

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]
-0.55	-0.88	-0.44	0.27	0.77	-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.698
r_dihedral_angle_4_deg	12.609
r_dihedral_angle_3_deg	9.068
r_long_range_B_refined	4.753
r_long_range_B_other	4.687
r_dihedral_angle_1_deg	2.403
r_scangle_other	2.403
r_mcangle_it	2.138
r_mcangle_other	2.138
r_scbond_it	1.453
r_scbond_other	1.453
r_angle_refined_deg	1.359
r_mcbond_it	1.279
r_mcbond_other	1.279
r_angle_other_deg	0.863
r_chiral_restr	0.076
r_gen_planes_refined	0.022
r_gen_planes_other	0.02
r_bond_refined_d	0.008
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	18305
Nucleic Acid Atoms
Solvent Atoms	1280
Heterogen Atoms	26

Software

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