5DOT | pdb_00005dot

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JDB	1JDB, 2YVQ
experimental model	PDB	2YVQ	1JDB, 2YVQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	294	20% PEG3350, 0.2 M tri-sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.337	α = 90
b = 133.482	β = 102.51
c = 142.907	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	CCD	ADSC QUANTUM 315r		2011-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.96112	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.4	139.516	96.3	0.114	0.135	0.071	7.9	3.5	136595	136595			28.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	83.4		0.342	0.342	0.212	2	3.5	17237

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	1JDB, 2YVQ	2.4	43.95	136557	6849	96.13	0.1662	0.1646	0.1721	0.1964	0.1693	RANDOM	40.365

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]
-0.21		-0.27	1.19		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.133
r_dihedral_angle_4_deg	15.823
r_dihedral_angle_3_deg	13.463
r_dihedral_angle_1_deg	5.708
r_mcangle_it	4.557
r_mcbond_it	2.929
r_mcbond_other	2.929
r_angle_refined_deg	1.293
r_angle_other_deg	0.835
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20944
Nucleic Acid Atoms
Solvent Atoms	819
Heterogen Atoms	46

Software

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