4AR1 | pdb_00004ar1

Crystal Structure of the Peptidase Domain of Collagenase H from Clostridium histolyticum at 2.01 Angstrom resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y3U	PDB ENTRY 2Y3U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.25		22.5% PEG3350 AND 0.15M SODIUM FORMATE, PH 7.25

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.05	α = 90
b = 108.23	β = 90
c = 51.27	γ = 90

Symmetry
Space Group	P 21 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	CCD	ADSC QUANTUM 315r		2011-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.01	46.33	99.8	0.14	7.8	5.8		29831		2	23.3

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	2.01	2.12	99.6		0.76	2	5.2

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	PDB ENTRY 2Y3U	2.01	46.33	28276	1511	99.65	0.20272	0.20028	0.2	0.24953	0.25	RANDOM	26.759

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]
0.78			1.55		-2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.139
r_sphericity_free	20.475
r_dihedral_angle_4_deg	19.851
r_dihedral_angle_3_deg	15.206
r_sphericity_bonded	8.327
r_dihedral_angle_1_deg	5.661
r_rigid_bond_restr	4.546
r_angle_refined_deg	0.988
r_angle_other_deg	0.829
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3106
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing