9HBA | pdb_00009hba

Crystal structure of C35 bound to Hem

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	3.0 M Ammonium sulfate; 1% (w/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.178	α = 90
b = 92.178	β = 90
c = 142.973	γ = 120

Symmetry
Space Group	P 32 2 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	PIXEL	DECTRIS EIGER2 X 16M		2023-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.51	53.255	100	0.095	0.097	0.022	1	14.5	20.1		110596

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	1.51	1.54			4.399	4.559	1.178	0.324	0.3	14.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.51	53.255	109875	5451	99.403	0.186	0.1844	0.1954	0.2149	0.2238	31.198

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]
0.63	0.315		0.63		-2.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.01
r_dihedral_angle_3_deg	14.686
r_dihedral_angle_2_deg	10.615
r_lrange_it	6.822
r_lrange_other	6.822
r_scangle_it	5.72
r_scangle_other	5.719
r_dihedral_angle_1_deg	5.286
r_scbond_it	4.16
r_scbond_other	4.16
r_mcangle_other	2.655
r_mcangle_it	2.654
r_mcbond_it	2.311
r_mcbond_other	2.267
r_angle_refined_deg	1.555
r_angle_other_deg	0.548
r_nbd_other	0.265
r_nbd_refined	0.256
r_symmetry_nbd_refined	0.251
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.127
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.069
r_xyhbond_nbd_other	0.057
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.009
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4363
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	412

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing