3QBP

Crystal structure of fumarase Fum from Mycobacterium marinum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NO9	pdb entry 3no9, molecule A residues 43 to 393

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	MymaA.01507.a.A1 PS00842 at 51.1 mg/mL against PACT screen condition A7, 0.2 M NaCl, 0.1 M NaOAc pH 5.0, 20% PEG 6000 soaked into PACT A7 with 25% EG as cryo-protectant, crystal tracking ID 218662a7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.88	α = 90
b = 114.08	β = 107.01
c = 98.84	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	CCD	ADSC QUANTUM 315r		2010-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97946	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.85	50	99.9	0.09	14.51	4.6	176835	176663		-3	22.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	100		0.505	3.1	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 3no9, molecule A residues 43 to 393	1.85	50	176519	8834	99.9	0.157	0.155	0.188	17.28

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]
-0.34		0.79	-0.75		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.664
r_dihedral_angle_4_deg	17.533
r_dihedral_angle_3_deg	12.559
r_dihedral_angle_1_deg	5.079
r_scangle_it	3.357
r_scbond_it	2
r_angle_refined_deg	1.314
r_mcangle_it	1.203
r_mcbond_it	0.689
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12804
Nucleic Acid Atoms
Solvent Atoms	1684
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction