3QL1 | pdb_00003ql1

Crystal Structure of Ribonuclease A Variant A4C/D83E/V118C

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RSA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	0.1M sodium acetate, 0.2 M ammonium sulfate, 25% (w/v) PEG 4000, 10mM copper chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.248	α = 90
b = 53.781	β = 117.95
c = 42.869	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 225 mm CCD		2010-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.29	35	90.6	0.051	11.31		27539	24943		-3	18.017

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.29	1.32	56		0.429	0.55	2.06

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	7RSA	1.29	32.24	24943	24943	1248	100	0.1555	0.1555	0.1536	0.1541	0.19	0.1861	RANDOM	14.7261

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]
0.29		0.03	-0.13		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.185
r_dihedral_angle_4_deg	20.077
r_sphericity_free	11.461
r_dihedral_angle_3_deg	10.445
r_sphericity_bonded	7.185
r_scangle_it	7.032
r_dihedral_angle_1_deg	6.096
r_scbond_it	5.12
r_mcangle_it	3.79
r_rigid_bond_restr	2.838
r_mcbond_it	2.669
r_angle_refined_deg	2.338
r_chiral_restr	0.142
r_bond_refined_d	0.025
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	952
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction