4J5K | pdb_00004j5k

Crystal structure analysis of Streptomyces aureofaciens ribonuclease Sa Y51F mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T2H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	Ammonium sulfate 0.9 M, phosphate buffer 0.1 M , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.303	α = 90
b = 63.813	β = 90
c = 77.624	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2002-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	1.1	EMBL/DESY, HAMBURG	X31

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	1.23	20	97.8	0.037	29.7	2.3	56065	54845

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	1.23	1.24	82.6		0.139	4.9	1.8	1493

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1T2H	1.23	18.59	56065	52028	2778	97.85	0.10569	0.10401	0.1036	0.13568	0.1358	RANDOM	11.99

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]
-0.04			0.03		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	47.348
r_dihedral_angle_2_deg	33.209
r_dihedral_angle_4_deg	19.366
r_sphericity_bonded	14.745
r_dihedral_angle_3_deg	10.54
r_dihedral_angle_1_deg	6.874
r_rigid_bond_restr	6.05
r_angle_refined_deg	2.108
r_angle_other_deg	1.469
r_chiral_restr	0.173
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1490
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	17

Software

Software
Software Name	Purpose
HKL-2000	data collection
model	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
model	phasing