3ECL | pdb_00003ecl

Carbonmonoxy Sperm Whale Myoglobin at 40 K: Laser on

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MBC	PDB ENTRY 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	34.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.31	α = 90
b = 30.63	β = 105.76
c = 63.729	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	40	CCD	MAR CCD 165 mm		2007-05-24	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	95.5	0.033	15.1	3.7		37319		-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	81.1		0.204		3.1	3122

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	PDB ENTRY 1MBC	1.21	19.93	37300	1875	95.68	0.145	0.143	0.14	0.179	0.18	RANDOM	13.262

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		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.934
r_dihedral_angle_4_deg	19.148
r_dihedral_angle_3_deg	13.743
r_sphericity_free	10.088
r_scangle_it	5.469
r_sphericity_bonded	5.454
r_dihedral_angle_1_deg	4.952
r_scbond_it	4.003
r_mcangle_it	2.891
r_rigid_bond_restr	2.473
r_mcbond_it	2.043
r_angle_refined_deg	1.933
r_nbtor_refined	0.319
r_nbd_refined	0.264
r_symmetry_vdw_refined	0.141
r_chiral_restr	0.135
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1217
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	55

Software

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