8FDJ

Wild-Type Sperm Whale Myoglobin in Complex with Nitrosobenzene

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	2.56 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.529	α = 90
b = 30.049	β = 104.55
c = 64.622	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 300K		2014-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	50	99.7	0.036	0.9	29.1	3.1		13162

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78			0.347	0.9

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	PDB entry 2MBW	1.75	33.44	12365	590	98.11	0.23098	0.22875	0.27612	RANDOM	21.128

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]
-0.2		0.05	0.16		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.369
r_dihedral_angle_4_deg	17.871
r_dihedral_angle_3_deg	14.649
r_dihedral_angle_1_deg	5.938
r_long_range_B_refined	4.442
r_long_range_B_other	4.437
r_scangle_other	3.587
r_mcangle_it	2.389
r_mcangle_other	2.388
r_scbond_other	2.311
r_scbond_it	2.308
r_mcbond_it	1.702
r_mcbond_other	1.674
r_angle_refined_deg	1.578
r_angle_other_deg	1.019
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.001
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	1203
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	56

Software

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