7EMV | pdb_00007emv

Crystal Structure of the HasAp V37G Mutant Capturing Iron-5,10,15-Triphenylporphyrin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XIC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	100mM Imidazole/HCl (pH 8.0), 30% PEG 8000, 0.2M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.347	α = 90
b = 84.347	β = 90
c = 45.735	γ = 90

Symmetry
Space Group	P 43 21 2

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	RAYONIX MX225-HS		2018-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.000	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.45	45.74	99.6	0.087	0.089	0.017	1	25	25.9		29690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47	92.9		1.461	1.519	0.409	0.552		13.5

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	5XIC	1.45	20	28084	1540	99.38	0.1319	0.1294	0.13	0.176	0.18	RANDOM	18.55

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]
0.29			0.29		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.914
r_dihedral_angle_3_deg	10.478
r_dihedral_angle_1_deg	6.691
r_rigid_bond_restr	4.238
r_dihedral_angle_4_deg	2.731
r_angle_refined_deg	1.888
r_angle_other_deg	1.658
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.914
r_dihedral_angle_3_deg	10.478
r_dihedral_angle_1_deg	6.691
r_rigid_bond_restr	4.238
r_dihedral_angle_4_deg	2.731
r_angle_refined_deg	1.888
r_angle_other_deg	1.658
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1326
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	60

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

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.