Experiment: 1X9F

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		3.8A in-house structure of full erythrocruorin

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	281	2.8M Na phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 281.0K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.225	α = 90
b = 172.071	β = 90
c = 202.886	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE	RIGAKU RAXIS IIC			M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200H	1.5418
2	SYNCHROTRON	APS BEAMLINE 14-BM-C	1.0000	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2	2.6	105.41				74920	74920

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.8 Structure of the whole molecule	2.6	105.41	74920	63085	3337	88.66	0.21481	0.21481	0.21316	0.21	0.24615	RANDOM	34.318

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]
-1.45			-0.87		2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.027
r_dihedral_angle_4_deg	22.066
r_dihedral_angle_3_deg	17.11
r_dihedral_angle_1_deg	4.236
r_angle_refined_deg	1.875
r_nbtor_refined	0.304
r_nbd_refined	0.297
r_symmetry_vdw_refined	0.287
r_metal_ion_refined	0.201
r_symmetry_hbond_refined	0.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.027
r_dihedral_angle_4_deg	22.066
r_dihedral_angle_3_deg	17.11
r_dihedral_angle_1_deg	4.236
r_angle_refined_deg	1.875
r_nbtor_refined	0.304
r_nbd_refined	0.297
r_symmetry_vdw_refined	0.287
r_metal_ion_refined	0.201
r_symmetry_hbond_refined	0.201
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14028
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	555

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
CNS	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.