7EMU | pdb_00007emu

Crystal Structure of the HasAp V37G Mutant Capturing Manganese Tetraphenylporphyrin

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.6	293	50mM Citric acid/NaOH (pH 3.6), 10% PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.037	α = 90
b = 62.233	β = 90
c = 63.383	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	PIXEL	DECTRIS EIGER X 4M		2019-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.000	SPring-8	BL26B1

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	1.35	39.8	99.9	0.045	0.047	0.012	1	27.8	14.4		45004

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	1.35	1.37	100		2.189	2.268	0.591	0.743		14.3

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	3ELL	1.35	39.8	42753	2192	99.82	0.1575	0.1558	0.16	0.1922	0.19	RANDOM	25.636

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]
-1.52			2.22		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.113
r_dihedral_angle_4_deg	21.051
r_dihedral_angle_3_deg	11.488
r_dihedral_angle_1_deg	6.259
r_rigid_bond_restr	1.57
r_angle_other_deg	1.502
r_angle_refined_deg	1.433
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.113
r_dihedral_angle_4_deg	21.051
r_dihedral_angle_3_deg	11.488
r_dihedral_angle_1_deg	6.259
r_rigid_bond_restr	1.57
r_angle_other_deg	1.502
r_angle_refined_deg	1.433
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	120
Heterogen Atoms	55

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.