4OF9 | pdb_00004of9

Structure of K42N variant of sperm whale myoglobin

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	2.7 M ammonium sulfate, 20 mM Tris, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.304	α = 90
b = 90.304	β = 90
c = 45.314	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	CCD	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00000	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.241	24.76	98.6	0.058	36.1	5.8		58965		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.241	1.273	90.4		0.209		2.1	3753

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	3OCK	1.241	24.76	55979	2983	98.76	0.11969	0.11854	0.12	0.14123	0.14	RANDOM	11.499

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]
0.08	0.08		0.08		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	52.813
r_dihedral_angle_2_deg	36.66
r_dihedral_angle_3_deg	13.116
r_sphericity_bonded	9.93
r_rigid_bond_restr	8.353
r_dihedral_angle_4_deg	5.437
r_dihedral_angle_1_deg	5.192
r_long_range_B_refined	4.706
r_long_range_B_other	3.202
r_angle_refined_deg	2.77
r_scangle_other	2.334
r_scbond_it	2.27
r_scbond_other	2.255
r_mcangle_it	1.814
r_mcangle_other	1.814
r_mcbond_it	1.347
r_mcbond_other	1.347
r_angle_other_deg	1.152
r_chiral_restr	0.19
r_bond_refined_d	0.028
r_gen_planes_refined	0.014
r_gen_planes_other	0.01
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1216
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	75

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling