2Q2N

Crystal structure of Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	30% PEG 2000, 0.1M Tris/HCl pH 8, 0.2M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.3	α = 90
b = 49.9	β = 90
c = 118.2	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	CCD	MARRESEARCH		2006-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.76	29.553	94.1	0.087	0.082	21.72	8.1		25719		5.5	27.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	2	96.4		0.37	0.306	5.55	5	7021

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1C1H	1.8	29.55	25617	1281	100	0.194	0.192	0.25	RANDOM	25.116

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]
0.81			-1.37		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.329
r_dihedral_angle_4_deg	14.999
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_1_deg	5.201
r_scangle_it	3.042
r_scbond_it	2.055
r_angle_refined_deg	1.525
r_mcangle_it	1.2
r_mcbond_it	0.764
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.329
r_dihedral_angle_4_deg	14.999
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_1_deg	5.201
r_scangle_it	3.042
r_scbond_it	2.055
r_angle_refined_deg	1.525
r_mcangle_it	1.2
r_mcbond_it	0.764
r_nbtor_refined	0.299
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.156
r_chiral_restr	0.116
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2486
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	48

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.