3WC6 | pdb_00003wc6

Carboxypeptidase B in complex with 2nd zinc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WAB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	296	100mM sodium cacodylate (pH 5.3-6.8), 100mM zinc acetate, 5-15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.05	α = 90
b = 79.05	β = 90
c = 100.719	γ = 90

Symmetry
Space Group	P 41 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	86	IMAGE PLATE	RIGAKU RAXIS II		2010-01-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.541865

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	15	94.1				36726

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.71	84.5

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	3WAB	1.65	15	36472	1811	93.53	0.1887	0.1867	0.1858	0.2287	0.2282	RANDOM	17.4876

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.081
r_dihedral_angle_4_deg	14.186
r_dihedral_angle_3_deg	12.711
r_dihedral_angle_1_deg	6.274
r_scangle_it	4.838
r_scbond_it	3.209
r_angle_refined_deg	1.973
r_mcangle_it	1.944
r_mcbond_it	1.257
r_chiral_restr	0.152
r_bond_refined_d	0.025
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2436
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	11

Software

Software
Software Name	Purpose
d*TREK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
RAPID-AUTO	data collection
d*TREK	data scaling
PHASER	phasing