3DKE | pdb_00003dke

Polar and non-polar cavities in phage T4 lysozyme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	277	2.0-2.2 M NaH2PO4 and K2HPO4, pH 6.9, 5mM BME, 5mM oxidized BME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.226	α = 90
b = 60.226	β = 90
c = 96.677	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 315		2007-01-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9796,0.9797,0.9742,0.9807	ALS	8.2.1

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	1.25	52.2	99.9	0.115	23.2	9.6		56299		2	11.6

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	1.25	1.27	100		0.214	13.9	7.1	2753

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.25	52.13	53423	2851	99.81	0.15626	0.15538	0.18	0.17281	RANDOM	14.834

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]
-0.6	-0.3		-0.6		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.99
r_dihedral_angle_4_deg	12.38
r_dihedral_angle_3_deg	9.729
r_dihedral_angle_1_deg	4.551
r_scangle_it	3.414
r_scbond_it	2.393
r_mcangle_it	1.152
r_angle_refined_deg	1.142
r_mcbond_it	0.671
r_nbtor_refined	0.306
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.069
r_metal_ion_refined	0.052
r_bond_refined_d	0.007
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_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	1305
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing