2VLZ | pdb_00002vlz

Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.8		BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS, 5-10% OF GLYCEROL PH 5.2)

Crystal Properties
Matthews coefficient	Solvent content
1.48	16.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.804	α = 90
b = 28.714	β = 105.82
c = 35.452	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	IMAGE PLATE	MARRESEARCH		2007-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM1A		ESRF	BM1A

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	1.38	34.16	99.5	0.06	6.41	3.59		20072

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	1.5	1.58	100		0.44	1.45	2.96

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GJN	1.5	26.87	19043	973	99.3	0.164	0.162	0.19	RANDOM	17.9

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]
-0.17		0.17	0.2		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.193
r_dihedral_angle_4_deg	15.603
r_dihedral_angle_3_deg	12.525
r_dihedral_angle_1_deg	4.371
r_scangle_it	2.856
r_scbond_it	1.878
r_angle_refined_deg	1.166
r_mcangle_it	1.107
r_mcbond_it	0.668
r_nbtor_refined	0.304
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.169
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.07
r_bond_refined_d	0.055
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1199
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing