1ZRS | pdb_00001zrs

wild-type LD-carboxypeptidase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	294	citric acid, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.185	α = 90
b = 78.271	β = 104.33
c = 71.258	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	CCD	MARRESEARCH		2004-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	1.5	20	97.1	0.037	0.037	20.9	2.2	86224	86224			16

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	1.5	1.52	95.1		0.252	0.252	4	2	3359

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MIRAS	THROUGHOUT	1.5	20	81899	81899	4325	97.18	0.16442	0.16442	0.16373	0.16	0.1773	0.18	RANDOM	13.085

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]
1.98		0.37	-0.65		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.72
r_scangle_it	4.194
r_scbond_it	2.508
r_mcangle_it	1.55
r_angle_refined_deg	1.46
r_mcbond_it	0.863
r_angle_other_deg	0.843
r_symmetry_vdw_other	0.333
r_nbd_other	0.255
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.092
r_nbtor_other	0.082
r_symmetry_hbond_refined	0.058
r_gen_planes_other	0.015
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	4505
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing