Experiment: 7VDN

High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	2.8 M ammonium sulfate, 50 mM K2HPO4, 50 mM NaH2PO4, 10% glycerol, 2 mg/ml sodium dithionite

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.403	α = 90
b = 30.702	β = 105.565
c = 63.804	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	PIXEL	DECTRIS PILATUS 200K		2016-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54056

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	0.93	20.02	100	0.114	0.124	0.047	0.998	9.7	11.9		86393			8.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.93	0.95	99.7		0.914	0.069	0.5	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1VXC	0.93	20.02	1.33	85826	4297	99.33	0.1882	0.187	0.1866	0.2105	0.2109	15.22

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.5982
f_angle_d	1.0838
f_chiral_restr	0.0775
f_bond_d	0.0084
f_plane_restr	0.0081

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1204
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	60

Software

Software
Software Name	Purpose
PHENIX	refinement
CrysalisPro	data collection
Coot	model building
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing