6CF0

Sperm Whale Myoglobin H64V Mutant with Nitrite

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2MGJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	2.64 M ammonium sulfate, 100 mM Tris-Cl, 1 mM EDTA

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.15	α = 90
b = 90.15	β = 90
c = 45.324	γ = 120

Symmetry
Space Group	P 6

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 PILATUS 300K		2017-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	1.641	78.07	100	0.12	0.054	5	4.7		20847

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.641	1.684					1537

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	2MGJ	1.64	78.07	19887	959	80.47	0.16669	0.16543	0.19325	RANDOM	17.575

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]
-0.05	-0.02		-0.05		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.755
r_dihedral_angle_4_deg	19.473
r_dihedral_angle_3_deg	13.658
r_long_range_B_refined	5.752
r_long_range_B_other	5.752
r_dihedral_angle_1_deg	5.196
r_scangle_other	4.179
r_scbond_it	3.518
r_scbond_other	2.903
r_mcangle_other	2.194
r_mcangle_it	2.185
r_angle_refined_deg	2.142
r_mcbond_it	1.513
r_mcbond_other	1.512
r_angle_other_deg	1.126
r_chiral_restr	0.152
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_gen_planes_other	0.007
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1214
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing