3KGQ | pdb_00003kgq

Carboxypeptidase A liganded to an organic small-molecule: conformational changes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CTB	PDB ENTRY 2CTB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	20% PEG 3350, 0.2M NH4Cl, 0.02M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.604	α = 90
b = 57.006	β = 102.04
c = 60.604	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	IMAGE PLATE	MAR555 FLAT PANEL	Mirrors	2009-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8150	EMBL/DESY, HAMBURG	X11

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	1.698	20.673	99.6	0.078	0.078	18.1	2.9		29594	3	3	25.4

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	1.7	1.79	99.8		0.28	0.28	2	3.1	4288

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2CTB	1.7	20.24	29594	27296	893	91.54	0.18	0.18	0.18	0.1788	0.204	0.2021	RANDOM	17.72

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]
0.03		0.22	-0.21		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.565
r_dihedral_angle_4_deg	15.692
r_dihedral_angle_3_deg	11.408
r_dihedral_angle_1_deg	5.33
r_scangle_it	1.876
r_scbond_it	1.147
r_angle_refined_deg	1.042
r_mcangle_it	0.795
r_mcbond_it	0.423
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2398
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	64

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AUTOMAR	data reduction