2ZRQ | pdb_00002zrq

Crystal structure of S324A-subtilisin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z2X	PDB ENTRY 2Z2X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	0.1M Sodium Acetate pH 5.0, 0.2M Ammonium Sulfate, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.188	α = 90
b = 60.925	β = 90
c = 92.277	γ = 90

Symmetry
Space Group	P 21 21 21

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	RIGAKU JUPITER 210		2008-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	2.15	50	99.4	0.084	30.6			14504

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)
	2.15	2.23	97.6		0.232	6.24

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 2Z2X	2.16	36.81	13655	716	98.95	0.14658	0.14397	0.1442	0.19652	0.197	RANDOM	19.062

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	38.658
r_dihedral_angle_4_deg	17.869
r_dihedral_angle_3_deg	14.429
r_dihedral_angle_1_deg	6.215
r_scangle_it	3.6
r_scbond_it	2.46
r_angle_refined_deg	1.525
r_mcangle_it	1.422
r_mcbond_it	0.886
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.178
r_metal_ion_refined	0.143
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2314
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing