1H87 | pdb_00001h87

Gadolinium derivative of tetragonal Hen Egg-White Lysozyme at 1.7 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LYT	PBD ENTRY 6LYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	293	NACL 0.8 M, SODIUM ACETATE 50 MM, PH4.5, GD-HP-DO3A 100MM, [PROT]=40 MG/ML, 293 K, pH 4.50

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.25	α = 90
b = 77.25	β = 90
c = 38.66	γ = 90

Symmetry
Space Group	P 43 21 2

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	MIRRORS	2000-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.72	17.2	99.5	0.059	8.1	12.5		12876		3	15.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.81	96.8		0.173	4	8.9

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	PBD ENTRY 6LYT	1.72	27.33	23249	2169	97.9	0.18	0.18	0.19	0.21	0.22	RANDOM	14.8

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]
-1.31			-1.31		2.62

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.2
c_angle_deg	1.5
c_scangle_it	1.23
c_scbond_it	0.87
c_improper_angle_d	0.83
c_mcangle_it	0.3
c_mcbond_it	0.17
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	62

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
SCALA	data scaling
CNS	phasing