2NRL | pdb_00002nrl

Blackfin tuna myoglobin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	0.2 M potassium/sodium tartrate, 0.1 M sodium citrate, and 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.985	α = 90
b = 51.976	β = 103.96
c = 38.781	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	CCD	MAR CCD 165 mm		2006-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.92	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	0.91	30	98.2	0.055	16	7.2	93820	92131			13.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	0.91	0.94	82.5		0.386	3.1	4	9383

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	1MYT	0.91	30	87322	4594	98.2	0.1487	0.1487	0.14	0.1487	0.14	RANDOM	11.218

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]
-0.12		-0.13	0.33		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.616
r_dihedral_angle_3_deg	10.468
r_sphericity_free	7.967
r_dihedral_angle_1_deg	4.62
r_dihedral_angle_4_deg	4.349
r_sphericity_bonded	3.781
r_scangle_it	3.297
r_scbond_it	2.452
r_mcangle_it	1.885
r_mcbond_it	1.579
r_rigid_bond_restr	1.559
r_angle_refined_deg	1.445
r_angle_other_deg	0.935
r_mcbond_other	0.578
r_nbd_refined	0.239
r_nbtor_refined	0.181
r_symmetry_vdw_other	0.173
r_nbd_other	0.161
r_xyhbond_nbd_refined	0.151
r_symmetry_vdw_refined	0.108
r_nbtor_other	0.092
r_chiral_restr	0.078
r_symmetry_hbond_refined	0.059
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1270
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing