3E55 | pdb_00003e55

Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser off

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	6	293	2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.319	α = 90
b = 30.604	β = 105.39
c = 63.618	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		2008-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW14A	0.827	Photon Factory	AR-NW14A

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	1.21	50	95.2	0.047	11.7	3.6		37156		-3

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)
	1.21	1.25	73.2		0.366		2.6	2822

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	1MBC	1.21	14.97	37141	1868	95.16	0.156	0.153	0.15	0.205	0.2	RANDOM	15.421

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]
0.01		-0.03	-0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.219
r_dihedral_angle_3_deg	12.896
r_dihedral_angle_4_deg	10.847
r_sphericity_free	10.495
r_sphericity_bonded	6.2
r_scangle_it	6.041
r_dihedral_angle_1_deg	5.159
r_scbond_it	4.58
r_mcangle_it	3.294
r_rigid_bond_restr	2.965
r_mcbond_it	2.353
r_angle_refined_deg	1.962
r_metal_ion_refined	0.653
r_nbtor_refined	0.319
r_nbd_refined	0.306
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.182
r_chiral_restr	0.145
r_xyhbond_nbd_refined	0.119
r_bond_refined_d	0.023
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1217
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	55

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling