3CDO | pdb_00003cdo

Bacteriophage T4 lysozyme mutant R96V in wildtype background at low temperature

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L63

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		100 MM MES, 200 MM LITHIUM SULFATE, 35% MPD, 50 MM 1,6-HEXANEDIOL, 12.5 MG/ML, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.82	α = 90
b = 99.316	β = 90
c = 123.012	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR scanner 345 mm plate		2001-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.87	23.881	99.1	0.059	0.059	10.5	3		58798		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.87	1.97	95.5		0.235	0.235	3.2	2.8

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1L63	1.87	23.82	57595	1134	99.1	0.187	0.187	0.19	0.231	RANDOM	17.477

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]
			0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.576
r_dihedral_angle_4_deg	16.409
r_dihedral_angle_3_deg	13.662
r_dihedral_angle_1_deg	4.709
r_scangle_it	2.632
r_scbond_it	1.668
r_angle_refined_deg	1.112
r_mcangle_it	0.956
r_mcbond_it	0.585
r_nbtor_refined	0.298
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.177
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5310
Nucleic Acid Atoms
Solvent Atoms	859
Heterogen Atoms	62

Software

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