3BZN | pdb_00003bzn

Crystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	6.5	298	well solution: 0.1M Bis-Tris pH 6.5, 20% PEG-MME 5000. protein solution: 50mM Tris pH 7.8, 50 mM magnesium sulfate. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.28	α = 90
b = 70.49	β = 90
c = 90.28	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	105	IMAGE PLATE	RIGAKU RAXIS IV++		2004-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.99	29.62	99.2	0.074	9.2	2.97		28882

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)
	1.99	2.07	95.7		0.322	3.2	2.82	2745

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	20	28501	1457	99.06	0.206	0.202	0.2	0.284	0.29	RANDOM	28.943

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]
-1.57			-0.65		2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.979
r_dihedral_angle_4_deg	22.582
r_dihedral_angle_3_deg	20.863
r_dihedral_angle_1_deg	7.444
r_scangle_it	4.242
r_scbond_it	2.975
r_angle_refined_deg	2.023
r_mcangle_it	1.746
r_mcbond_it	1.091
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.979
r_dihedral_angle_4_deg	22.582
r_dihedral_angle_3_deg	20.863
r_dihedral_angle_1_deg	7.444
r_scangle_it	4.242
r_scbond_it	2.975
r_angle_refined_deg	2.023
r_mcangle_it	1.746
r_mcbond_it	1.091
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.297
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.154
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3482
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	16

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.